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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

    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 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

  3. Effect of Volume-of-Interest Misregistration on Quantitative Planar Activity and Dose Estimation

    PubMed Central

    Song, N.; He, B.; Frey, E. C.

    2010-01-01

    In targeted radionuclide therapy (TRT), dose estimation is essential for treatment planning and tumor dose response studies. Dose estimates are typically based on a time series of whole body conjugate view planar or SPECT scans of the patient acquired after administration of a planning dose. Quantifying the activity in the organs from these studies is an essential part of dose estimation. The Quantitative Planar (QPlanar) processing method involves accurate compensation for image degrading factors and correction for organ and background overlap via the combination of computational models of the image formation process and 3D volumes of interest defining the organs to be quantified. When the organ VOIs are accurately defined, the method intrinsically compensates for attenuation, scatter, and partial volume effects, as well as overlap with other organs and the background. However, alignment between the 3D organ volume of interest (VOIs) used in QPlanar processing and the true organ projections in the planar images is required. The goal of this research was to study the effects of VOI misregistration on the accuracy and precision of organ activity estimates obtained using the QPlanar method. In this work, we modeled the degree of residual misregistration that would be expected after an automated registration procedure by randomly misaligning 3D SPECT/CT images, from which the VOI information was derived, and planar images. Mutual information based image registration was used to align the realistic simulated 3D SPECT images with the 2D planar images. The residual image misregistration was used to simulate realistic levels of misregistration and allow investigation of the effects of misregistration on the accuracy and precision of the QPlanar method. We observed that accurate registration is especially important for small organs or ones with low activity concentrations compared to neighboring organs. In addition, residual misregistration gave rise to a loss of precision

  4. Effects of shortened acquisition time on accuracy and precision of quantitative estimates of organ activity1

    PubMed Central

    He, Bin; Frey, Eric C.

    2010-01-01

    Purpose: Quantitative estimation of in vivo organ uptake is an essential part of treatment planning for targeted radionuclide therapy. This usually involves the use of planar or SPECT scans with acquisition times chosen based more on image quality considerations rather than the minimum needed for precise quantification. In previous simulation studies at clinical count levels (185 MBq 111In), the authors observed larger variations in accuracy of organ activity estimates resulting from anatomical and uptake differences than statistical noise. This suggests that it is possible to reduce the acquisition time without substantially increasing the variation in accuracy. Methods: To test this hypothesis, the authors compared the accuracy and variation in accuracy of organ activity estimates obtained from planar and SPECT scans at various count levels. A simulated phantom population with realistic variations in anatomy and biodistribution was used to model variability in a patient population. Planar and SPECT projections were simulated using previously validated Monte Carlo simulation tools. The authors simulated the projections at count levels approximately corresponding to 1.5–30 min of total acquisition time. The projections were processed using previously described quantitative SPECT (QSPECT) and planar (QPlanar) methods. The QSPECT method was based on the OS-EM algorithm with compensations for attenuation, scatter, and collimator-detector response. The QPlanar method is based on the ML-EM algorithm using the same model-based compensation for all the image degrading effects as the QSPECT method. The volumes of interests (VOIs) were defined based on the true organ configuration in the phantoms. The errors in organ activity estimates from different count levels and processing methods were compared in terms of mean and standard deviation over the simulated phantom population. Results: There was little degradation in quantitative reliability when the acquisition time was

  5. Acute toxicity estimation by calculation--Tubifex assay and quantitative structure-activity relationships.

    PubMed

    Tichý, Milon; Rucki, Marian; Hanzlíková, Iveta; Roth, Zdenek

    2008-11-01

    A quantitative structure-activity relationship (QSAR) model dependent on log P(n - octanol/water), or log P(OW), was developed with acute toxicity index EC50, the median effective concentration measured as inhibition of movement of the oligochaeta Tubifex tubifex with 3 min exposure, EC50(Tt) (mol/L): log EC50(Tt) = -0.809 (+/-0.035) log P(OW) - 0.495 (+/-0.060), n=82, r=0.931, r2=0.867, residual standard deviation of the estimate 0.315. A learning series for the QSAR model with the oligochaete contained alkanols, alkenols, and alkynols; saturated and unsaturated aldehydes; aniline and chlorinated anilines; phenol and chlorinated phenols; and esters. Three cross-validation procedures proved the robustness and stability of QSAR models with respect to the chemical structure of compounds tested within a series of compounds used in the learning series. Predictive ability was described by q2 .801 (cross-validated r2; predicted variation estimated with cross-validation) in LSO (leave-a structurally series-out) cross-validation. PMID:18522479

  6. [Quantitative estimation of connection of the heart rate rhythm with motor activity in rat fetuses].

    PubMed

    Vdovichenko, N D; Timofeeva, O P; Bursian, A V

    2014-01-01

    In rat fetuses at E17-20 with preserved placental circulation with use of mathematical analysis there were revealed value and character of connections of slow wave oscillations of the heart rhythm with motor activity for 30 min of observation. In the software "PowerGraph 3.3.8", normalization and filtration of the studied signals were performed at three frequency diapasons: D1 - 0.02-0.2 Hz (5-50 s), D2 - 0.0083-0.02 Hz (50 s-2 min), and D3 - 0.0017-0.0083 Hz (2-10 min). The EMG curves filtrated by diapasons or piezograms were compared with periodograms in the corresponding diapasons of the heart rhythm variations. In the software "Origin 8.0", quantitative estimation of the degree of intersystemic interrelations for each frequency diapason was performed by Pearson correlation of coefficient, by the correlation connection value, and by the time shift of maximum of cross-correlation function. It has been established that in the frequency D1, regardless of age, the connection of heart rhythm oscillations with motor activity is expressed weakly. In the frequency diapason D2, the connection in most cases is located in the zone of weak and moderate correlations. In the multiminute diapason (D3), the connection is more pronounced. The number of animals that have a significant value of the correlation connection rises. The fetal MA fires in the decasecond diapason in all age groups are accompanied by short-time decelerations of the heart rhythms. In the minute diapason, there is observed a transition from positive connections at E17 and E18 to the negative ones at E19-20. Results of the study are considered in association with age-related changes of ratios of positive and negative oscillations of the heart rhythm change depending on the character of motor activity. PMID:25486813

  7. 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

  8. 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.

  9. Estimating the persistence of organic contaminants in indirect potable reuse systems using quantitative structure activity relationship (QSAR).

    PubMed

    Lim, Seung Joo; Fox, Peter

    2012-09-01

    Predictions from the quantitative structure activity relationship (QSAR) model EPI Suite were modified to estimate the persistence of organic contaminants in indirect potable reuse systems. The modified prediction included the effects of sorption, biodegradation, and oxidation that may occur during sub-surface transport. A retardation factor was used to simulate the mobility of adsorbed compounds during sub-surface transport to a recovery well. A set of compounds with measured persistent properties during sub-surface transport was used to validate the results of the modifications to the predictions of EPI Suite. A comparison of the predicted values and measured values was done and the residual sum of the squares showed the importance of including oxidation and sorption. Sorption was the most important factor to include in predicting the fates of organic chemicals in the sub-surface environment. PMID:22766422

  10. 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...

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

    PubMed Central

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

    2009-01-01

    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

  12. 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

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

    PubMed

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

    2009-02-01

    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

  14. The Impact of 3D Volume-of-Interest Definition on Accuracy and Precision of Activity Estimation in Quantitative SPECT and Planar Processing Methods

    PubMed Central

    He, Bin; Frey, Eric C.

    2010-01-01

    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 effect 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 estimations. 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 the same transaxial plane 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 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

  15. 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

  16. 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

  17. 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.

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

    NASA Astrophysics Data System (ADS)

    Pechurkin, N. S.

    It's necessary to have quantitative criteria to elaborate efficient artificial ecosystems (AES). As usual, these criteria are connected with exact objectives of AES designed. For example, if AES is considered for use in space, it's to be efficient in its use of mass, power, volume (size) and human labor and to be reliable. Another task arises: how to determine, to find out the quantitative criteria for natural ecosystems functioning. To solve the problem, it's fruitful to use a hierarchical approach suitable for both individual links and ecosystem as a whole. Energy fluxes criteria (principles) were developed to estimate the functional activities of biosystems at populations, communities and ecosystems levels. Major feature of ecosystem as a whole is a 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: energy fluxes used by the biosystem and quantity of limiting substance included into its turnover. The use (utilization) of energy fluxes by ecosystem can be easily measured as a net primary production of photosynthesis (NPP). So, the ratio of 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 functioning, including 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.

  19. Thermal diffusivity estimation with quantitative pulsed phase thermography

    NASA Astrophysics Data System (ADS)

    Ospina-Borras, J. E.; Florez-Ospina, Juan F.; Benitez-Restrepo, H. D.; Maldague, X.

    2015-05-01

    Quantitative Pulsed Phase Thermography (PPT) has been only used to estimate defect parameters such as depth and thermal resistance. Here, we propose a thermal quadrupole based method that extends quantitative pulsed phase thermography. This approach estimates thermal diffusivity by solving a inversion problem based on non-linear squares estimation. This approach is tested with pulsed thermography data acquired from a composite sample. We compare our results with another technique established in time domain. The proposed quantitative analysis with PPT provides estimates of thermal diffusivity close to those obtained with the time domain approach. This estimation requires only the a priori knowledge of sample thickness.

  20. 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.

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

    NASA Astrophysics Data System (ADS)

    Pechurkin, N. S.

    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, EUSED - is determined from the photoassimilation of CO 2 by plants (per time unit). It can be approximately estimated as the net primary production of photosynthesis (NPP). So, the ratio of CO 2 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.

  2. Probabilistic Quantitative Precipitation Estimates with Ground-based Radar Networks

    NASA Astrophysics Data System (ADS)

    Kirstetter, Pierre-Emmanuel; Gourley, Jonathan; Hong, Yang; Zhang, Jian; Moazamigoodarzi, Saber; Langston, Carrie; Arthur, Ami

    2015-04-01

    The uncertainty structure of radar quantitative precipitation estimation (QPE) is largely unknown at fine spatiotemporal scales near the radar measurement scale (1-km/5-min). By using the WSR-88D radar network and rain gauge datasets across the conterminous US, an investigation of this subject has been carried out within the framework of the NOAA/NSSL ground radar-based Multi-Radar Multi-Sensor. Probability distributions of precipitation rates are computed instead of deterministic values using a model quantifying the relation between radar reflectivity and the corresponding "true" precipitation. The probabilistic model considers multiple sources of error in radar QPE as well as the impacts of correction algorithms on the radar signal. Ensembles of reflectivity-to-rain rate relationships accounting explicitly for rain typology were derived at a 5-min/1-km scale. This approach preserves the fine space/time sampling properties of the radar and conditions probabilistic QPE on the rain rate and precipitation type when computing probabilistic quantitative precipitation estimates (PQPE). The model components were estimated on the basis of a 1-year-long data sample. This PQPE model provides the basis for precipitation probability maps and the generation of radar precipitation ensembles. Maps of the precipitation exceedance probability for specific thresholds (e.g. precipitation return periods) are demonstrated. Precipitation probability maps are accumulated to the hourly time scale and compare positively to the deterministic QPE. This approach to PQPE can readily apply to other systems including space-based passive and active sensor algorithms.

  3. The Mapping Model: A Cognitive Theory of Quantitative Estimation

    ERIC Educational Resources Information Center

    von Helversen, Bettina; Rieskamp, Jorg

    2008-01-01

    How do people make quantitative estimations, such as estimating a car's selling price? Traditionally, linear-regression-type models have been used to answer this question. These models assume that people weight and integrate all information available to estimate a criterion. The authors propose an alternative cognitive theory for quantitative…

  4. 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

  5. Uncertainty estimations for quantitative in vivo MRI T1 mapping

    NASA Astrophysics Data System (ADS)

    Polders, Daniel L.; Leemans, Alexander; Luijten, Peter R.; Hoogduin, Hans

    2012-11-01

    Mapping the longitudinal relaxation time (T1) of brain tissue is of great interest for both clinical research and MRI sequence development. For an unambiguous interpretation of in vivo variations in T1 images, it is important to understand the degree of variability that is associated with the quantitative T1 parameter. This paper presents a general framework for estimating the uncertainty in quantitative T1 mapping by combining a slice-shifted multi-slice inversion recovery EPI technique with the statistical wild-bootstrap approach. Both simulations and experimental analyses were performed to validate this novel approach and to evaluate the estimated T1 uncertainty in several brain regions across four healthy volunteers. By estimating the T1 uncertainty, it is shown that the variation in T1 within anatomic regions for similar tissue types is larger than the uncertainty in the measurement. This indicates that heterogeneity of the inspected tissue and/or partial volume effects can be the main determinants for the observed variability in the estimated T1 values. The proposed approach to estimate T1 and its uncertainty without the need for repeated measurements may also prove to be useful for calculating effect sizes that are deemed significant when comparing group differences.

  6. Uncertainty estimations for quantitative in vivo MRI T1 mapping.

    PubMed

    Polders, Daniel L; Leemans, Alexander; Luijten, Peter R; Hoogduin, Hans

    2012-11-01

    Mapping the longitudinal relaxation time (T(1)) of brain tissue is of great interest for both clinical research and MRI sequence development. For an unambiguous interpretation of in vivo variations in T(1) images, it is important to understand the degree of variability that is associated with the quantitative T(1) parameter. This paper presents a general framework for estimating the uncertainty in quantitative T(1) mapping by combining a slice-shifted multi-slice inversion recovery EPI technique with the statistical wild-bootstrap approach. Both simulations and experimental analyses were performed to validate this novel approach and to evaluate the estimated T(1) uncertainty in several brain regions across four healthy volunteers. By estimating the T(1) uncertainty, it is shown that the variation in T(1) within anatomic regions for similar tissue types is larger than the uncertainty in the measurement. This indicates that heterogeneity of the inspected tissue and/or partial volume effects can be the main determinants for the observed variability in the estimated T(1) values. The proposed approach to estimate T(1) and its uncertainty without the need for repeated measurements may also prove to be useful for calculating effect sizes that are deemed significant when comparing group differences. PMID:23041796

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Quantitative assessment of growth plate activity

    SciTech Connect

    Harcke, H.T.; Macy, N.J.; Mandell, G.A.; MacEwen, G.D.

    1984-01-01

    In the immature skeleton the physis or growth plate is the area of bone least able to withstand external forces and is therefore prone to trauma. Such trauma often leads to premature closure of the plate and results in limb shortening and/or angular deformity (varus or valgus). Active localization of bone seeking tracers in the physis makes bone scintigraphy an excellent method for assessing growth plate physiology. To be most effective, however, physeal activity should be quantified so that serial evaluations are accurate and comparable. The authors have developed a quantitative method for assessing physeal activity and have applied it ot the hip and knee. Using computer acquired pinhole images of the abnormal and contralateral normal joints, ten regions of interest are placed at key locations around each joint and comparative ratios are generated to form a growth plate profile. The ratios compare segmental physeal activity to total growth plate activity on both ipsilateral and contralateral sides and to adjacent bone. In 25 patients, ages 2 to 15 years, with angular deformities of the legs secondary to trauma, Blount's disease, and Perthes disease, this technique is able to differentiate abnormal segmental physeal activity. This is important since plate closure does not usually occur uniformly across the physis. The technique may permit the use of scintigraphy in the prediction of early closure through the quantitative analysis of serial studies.

  12. 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.

  13. 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.

  14. 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.

  15. Probabilistic quantitative precipitation estimation using dual polarization radar measurements

    NASA Astrophysics Data System (ADS)

    Lim, S.; Noh, S.; Lee, D.

    2013-12-01

    Weather radars have become a popular tool for meteorological applications such as quantitative precipitation estimation (QPE) with high spatiotemporal resolution. Especially, in the last decade, QPE performance has been improved by introduction of polarimetric technology. However, QPEs using dual polarization radar data are still subject to uncertainties resulted in rainfall conversion relationships, combination methods of different parameters, and sampling errors. Deterministic QPE typically based on decision tree method ignores such uncertainties which exacerbate performance in hydrologic flood forecasting. Probabilistic precipitation models provide an alternative framework for QPE to understand temporal and spatial variations of uncertainty. In this study, we propose a probabilistic QPE method from dual polarization radar measurements via data assimilation. The proposed method utilizes QPE ensembles based on different parameters of a polarimetric radar considering uncertainty of conversion equations and rainfall parameters. Ground observations are assimilated with QPE ensembles at each measurement time step. Rejection sampling based on Bayesian filtering is implemented to estimate posterior distribution of QPE and compare multiple models. The strength of the proposed method is that it can improve accuracy of QPE compared to deterministic QPE, identify uncertainty of QPE, and provide sound spatial precipitation fields including error structure, which is essential for hydrological data assimilation to improve flood forecasting. The real experiments are implemented to demonstrate applicability of this method using S-band dual polarization radar located in Mt. Biseul, Korea. The discussion will be focused on analysis of multi-model selection results by Bayesian filtering and comparison of accuracy between deterministic and probabilistic QPE methods.

  16. Estimation of Methanogen Biomass by Quantitation of Coenzyme M

    PubMed Central

    Elias, Dwayne A.; Krumholz, Lee R.; Tanner, Ralph S.; Suflita, Joseph M.

    1999-01-01

    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. We standardized a simple method for estimating methanogen biomass in a variety of environmental matrices. In this procedure we used the thiol biomarker coenzyme M (CoM) (2-mercaptoethanesulfonic acid), which is known to be present in all methanogenic bacteria. A high-performance liquid chromatography-based method for detecting thiols in pore water (A. Vairavamurthy and M. Mopper, Anal. Chim. Acta 78:363–370, 1990) 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. We 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. PMID:10584015

  17. Quantitative modeling of multiscale neural activity

    NASA Astrophysics Data System (ADS)

    Robinson, Peter A.; Rennie, Christopher J.

    2007-01-01

    The electrical activity of the brain has been observed for over a century and is widely used to probe brain function and disorders, chiefly through the electroencephalogram (EEG) recorded by electrodes on the scalp. However, the connections between physiology and EEGs have been chiefly qualitative until recently, and most uses of the EEG have been based on phenomenological correlations. A quantitative mean-field model of brain electrical activity is described that spans the range of physiological and anatomical scales from microscopic synapses to the whole brain. Its parameters measure quantities such as synaptic strengths, signal delays, cellular time constants, and neural ranges, and are all constrained by independent physiological measurements. Application of standard techniques from wave physics allows successful predictions to be made of a wide range of EEG phenomena, including time series and spectra, evoked responses to stimuli, dependence on arousal state, seizure dynamics, and relationships to functional magnetic resonance imaging (fMRI). Fitting to experimental data also enables physiological parameters to be infered, giving a new noninvasive window into brain function, especially when referenced to a standardized database of subjects. Modifications of the core model to treat mm-scale patchy interconnections in the visual cortex are also described, and it is shown that resulting waves obey the Schroedinger equation. This opens the possibility of classical cortical analogs of quantum phenomena.

  18. 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.

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

    PubMed

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

    2015-08-21

    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. PMID:26247228

  20. 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

  1. A method for quantitatively estimating diffuse and discrete hydrothermal discharge

    NASA Astrophysics Data System (ADS)

    Baker, Edward T.; Massoth, Gary J.; Walker, Sharon L.; Embley, Robert W.

    1993-07-01

    Submarine hydrothermal fluids discharge as undiluted, high-temperature jets and as diffuse, highly diluted, low-temperature percolation. Estimates of the relative contribution of each discharge type, which are important for the accurate determination of local and global hydrothermal budgets, are difficult to obtain directly. In this paper we describe a new method of using measurements of hydrothermal tracers such as Fe/Mn, Fe/heat, and Mn/heat in high-temperature fluids, low-temperature fluids, and the neutrally buoyant plume to deduce the relative contribution of each discharge type. We sampled vent fluids from the north Cleft vent field on the Juan de Fuca Ridge in 1988, 1989 and 1991, and plume samples every year from 1986 to 1991. The tracers were, on average, 3 to 90 times greater in high-temperature than in low-temperature fluids, with plume values intermediate. A mixing model calculates that high-temperature fluids contribute only ˜ 3% of the fluid mass flux but > 90% of the hydrothermal Fe and > 60% of the hydrothermal Mn to the overlying plume. Three years of extensive camera-CTD sled tows through the vent field show that diffuse venting is restricted to a narrow fissure zone extending for 18 km along the axial strike. Linear plume theory applied to the temperature plumes detected when the sled crossed this zone yields a maximum likelihood estimate for the diffuse heat flux of8.9 × 10 4 W/m, for a total flux of 534 MW, considering that diffuse venting is active along only one-third of the fissure system. For mean low- and high-temperature discharge of 25°C and 319°C, respectively, the discrete heat flux must be 266 MW to satisfy the mass flux partitioning. If the north Cleft vent field is globally representative, the assumption that high-temperature discharge dominates the mass flux in axial vent fields leads to an overestimation of the flux of many non-conservative hydrothermal species by about an order of magnitude.

  2. Estimation of crack and damage progression in concrete by quantitative acoustic emission analysis

    SciTech Connect

    Ohtsu, Masayasu

    1999-05-01

    The kinematics of cracking can be represented by the moment tensor. To distinguish moment tensor components from acoustic emission waveforms, the SiGMA (simplified Green`s functions for moment tensor analysis) procedure was developed. By applying the procedure to bending tests of notched beams, cracks in the fracture process zone of cementitious materials can be identified by kinematic means. In addition to cracks, estimation of the damage level in structural concrete is also conducted, based on acoustic emission activity of a concrete sample under compression. Depending on the damage resulting from existing microcracks, acoustic emission generated behavior is quantitatively estimated by the rate process analysis. The damage mechanics are introduced to quantify the degree of damage. Determining the current damage level using acoustic emission without information on undamaged concrete is attempted by correlating the damage value with the rate process.

  3. 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

  4. Quantitative structure-activity studies on monoamine oxidase inhibitors.

    PubMed

    Johnson, C L

    1976-05-01

    Quantitative structure-activity studies were carried out on a series of N-isopropylaryl hydrazides which inhibits monoamine oxidase (MAO). The inhibitory potencies of these compounds of MAO were found to correlate with the electron-withdrawing capacity of the aryl ring substituents as estimated by both empirical Hammet sigma constants and electronic indices from molecular orbital calculations. Based on these correlations and previously published data on other classes of MAO inhibitors, a general model for the inhibitor pharmacophore is proposed: potent MAO of an aromatic ring; electron-withdrawing groups on the aromatic ring or replacing the phenyl ring with certain types of heterocyclic rings will tend to increase the potency. PMID:1271400

  5. 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.

  6. 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

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

    PubMed

    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

  8. Quantitative abundance estimates from bidirectional reflectance measurements. [for planetary surfaces

    NASA Technical Reports Server (NTRS)

    Mustard, John F.; Pieters, Carle M.

    1987-01-01

    A simplified approach for estimating mineral abundances in mineral mixtures from bidirectional reflectance measurements is presented. Fundamental to this approach is a priori information concerning reflectance spectra of the individual minerals and an estimate of the particle sizes of the components. Simplified equations for bidirectional reflectance are used to linearize the systematics of spectral mixing. The method was used to determine the relative proportions of olivine, magnetite, enstatite, and anorthite in a mixture; the mass fractions of mixture components were calculated on the basis of known particle diameters. The results indicate that for materials without strongly adsorbing components, the accuracy of abundance determinations is better than 5 percent.

  9. The Centiloid Project: Standardizing Quantitative Amyloid Plaque Estimation by PET

    PubMed Central

    Klunk, William E.; Koeppe, Robert A.; Price, Julie C.; Benzinger, Tammie; Devous, Michael D.; Jagust, William; Johnson, Keith; Mathis, Chester A.; Minhas, Davneet; Pontecorvo, Michael J.; Rowe, Christopher C.; Skovronsky, Daniel; Mintun, Mark

    2014-01-01

    Although amyloid imaging with PiB-PET, and now with F-18-labelled tracers, has produced remarkably consistent qualitative findings across a large number of centers, there has been considerable variability in the exact numbers reported as quantitative outcome measures of tracer retention. In some cases this is as trivial as the choice of units, in some cases it is scanner dependent, and of course, different tracers yield different numbers. Our working group was formed to standardize quantitative amyloid imaging measures by scaling the outcome of each particular analysis method or tracer to a 0 to 100 scale, anchored by young controls (≤45 years) and typical Alzheimer’s disease patients. The units of this scale have been named “Centiloids.” Basically, we describe a “standard” method of analyzing PiB PET data and then a method for scaling any “non-standard” method of PiB PET analysis (or any other tracer) to the Centiloid scale. PMID:25443857

  10. 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

  11. A NOVEL TECHNIQUE FOR QUANTITATIVE ESTIMATION OF UPTAKE OF DIESEL EXHAUST PARTICLES BY LUNG CELLS

    EPA Science Inventory

    While airborne particulates like diesel exhaust particulates (DEP) exert significant toxicological effects on lungs, quantitative estimation of accumulation of DEP inside lung cells has not been reported due to a lack of an accurate and quantitative technique for this purpose. I...

  12. [Quantitative estimation of evapotranspiration from Tahe forest ecosystem, Northeast China].

    PubMed

    Qu, Di; Fan, Wen-Yi; Yang, Jin-Ming; Wang, Xu-Peng

    2014-06-01

    Evapotranspiration (ET) is an important parameter of agriculture, meteorology and hydrology research, and also an important part of the global hydrological cycle. This paper applied the improved DHSVM distributed hydrological model to estimate daily ET of Tahe area in 2007 using leaf area index and other surface data extracted TM remote sensing data, and slope, aspect and other topographic indices obtained by using the digital elevation model. The relationship between daily ET and daily watershed outlet flow was built by the BP neural network, and a water balance equation was established for the studied watershed, together to test the accuracy of the estimation. The results showed that the model could be applied in the study area. The annual total ET of Tahe watershed was 234.01 mm. ET had a significant seasonal variation. The ET had the highest value in summer and the average daily ET value was 1.56 mm. The average daily ET in autumn and spring were 0.30, 0.29 mm, respectively, and winter had the lowest ET value. Land cover type had a great effect on ET value, and the broadleaf forest had a higher ET ability than the mixed forest, followed by the needle leaf forest. PMID:25223020

  13. Quantitative estimate of the effect of cellulase components during degradation of cotton fibers.

    PubMed

    Wang, Lu-Shan; Zhang, Yu-Zhong; Yang, Hong; Gao, Pei-Ji

    2004-03-15

    A comprehensive mechanistic kinetic model for enzymatic degradation of cotton fibers has been established based on a complete factorial experiment in combination with multivariate stepwise regression analysis. The analysis of the statistical parameter value in the model suggests that the enzymatic degradation of cotton fiber is a progressive and heterogeneous process that includes, at least, two courses that occur sequentially and then progress in parallel. Cellulose fibers were first depolymerized or solubilized by the synergism between cellobiohydrolase I (CBHI) and endoglucanase I (EGI), and then the oligomers obtained were randomly hydrolyzed into glucose by EGI and beta-glucosidase. The proposed model can be applied to the quantitative estimation of the effects of three cellulase components, CBHI, EGI, and beta-glucosidase separately, or in combination during the entire process of cellulose degradation. The validity of the proposed model has been verified by a filter paper activity assay. Its other applicability was also discussed. PMID:14980825

  14. 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.

  15. "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…

  16. 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

  17. 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

  18. 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

  19. Quantitative risk estimation for a Legionella pneumophila infection due to whirlpool use.

    PubMed

    Bouwknegt, Martijn; Schijven, Jack F; Schalk, Johanna A C; de Roda Husman, Ana Maria

    2013-07-01

    Quantitative microbiological risk assessment was used to quantify the risk associated with the exposure to Legionella pneumophila in a whirlpool. Conceptually, air bubbles ascend to the surface, intercepting Legionella from the traversed water. At the surface the bubble bursts into dominantly noninhalable jet drops and inhalable film drops. Assuming that film drops carry half of the intercepted Legionella, a total of four (95% interval: 1-9) and 4.5×10(4) (4.4×10(4) - 4.7×10(4) ) cfu/min were estimated to be aerosolized for concentrations of 1 and 1,000 legionellas per liter, respectively. Using a dose-response model for guinea pigs to represent humans, infection risks for active whirlpool use with 100 cfu/L water for 15 minutes were 0.29 (∼0.11-0.48) for susceptible males and 0.22 (∼0.06-0.42) for susceptible females. A L. pneumophila concentration of ≥1,000 cfu/L water was estimated to nearly always cause an infection (mean: 0.95; 95% interval: 0.9-∼1). Estimated infection risks were time-dependent, ranging from 0.02 (0-0.11) for 1-minute exposures to 0.93 (0.86-0.97) for 2-hour exposures when the L. pneumophila concentration was 100 cfu/L water. Pool water in Dutch bathing establishments should contain <100 cfu Legionella/L water. This study suggests that stricter provisions might be required to assure adequate public health protection. PMID:23078231

  20. 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

  1. 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…

  2. Quantitative Estimation of Thermal Contact Conductance for a Real Front-end Component

    NASA Astrophysics Data System (ADS)

    Sano, Mutsumi; Takahashi, Sunao; Mochizuki, Tetsuro; Watanabe, Atsuo; Oura, Masaki; Kitamura, Hideo

    2007-01-01

    The thermal contact conductance (TCC) of a real front-end component at SPring-8 was estimated quantitatively by comparing the results of the experiments and those of the finite element analyses. This study contributes to the ongoing program to inquire into the real thermal resistance including the life of all front-end high-heat-load components.

  3. Quantitative Estimates of the Social Benefits of Learning, 1: Crime. Wider Benefits of Learning Research Report.

    ERIC Educational Resources Information Center

    Feinstein, Leon

    The cost benefits of lifelong learning in the United Kingdom were estimated, based on quantitative evidence. Between 1975-1996, 43 police force areas in England and Wales were studied to determine the effect of wages on crime. It was found that a 10 percent rise in the average pay of those on low pay reduces the overall area property crime rate by…

  4. 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...

  5. 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.

  6. QUANTITATIVE GENETIC ACTIVITY GRAPHICAL PROFILES FOR USE IN CHEMICAL EVALUATION

    EPA Science Inventory

    A graphic approach termed a Genetic Activity Profile (GAP) has been developed to display a matrix of data on the genetic and related effects of selected chemical agents. he profiles provide a visual overview of the quantitative (doses) and qualitative (test results) data for each...

  7. Estimating Cell Concentration in Three-Dimensional Engineered Tissues using High Frequency Quantitative Ultrasound

    PubMed Central

    Mercado, Karla P.; Helguera, Marίa; Hocking, Denise C.; Dalecki, Diane

    2015-01-01

    Histology and biochemical assays are standard techniques for estimating cell concentration in engineered tissues. However, these techniques are destructive and cannot be used for longitudinal monitoring of engineered tissues during fabrication processes. The goal of this study was to develop high-frequency quantitative ultrasound techniques to nondestructively estimate cell concentration in three-dimensional (3-D) engineered tissue constructs. High-frequency ultrasound backscatter measurements were obtained from cell-embedded, 3-D agarose hydrogels. Two broadband single-element transducers (center frequencies of 30 and 38 MHz) were employed over the frequency range of 13 to 47 MHz. Agarose gels with cell concentrations ranging from 1×104 to 1×106 cells mL−1 were investigated. The integrated backscatter coefficient (IBC), a quantitative ultrasound spectral parameter, was calculated and used to estimate cell concentration. Accuracy and precision of this technique were analyzed by calculating the percent error and coefficient of variation of cell concentration estimates. The IBC increased linearly with increasing cell concentration. Axial and lateral dimensions of regions of interest that resulted in errors of less than 20% were determined. Images of cell concentration estimates were employed to visualize quantitatively regional differences in cell concentrations. This ultrasound technique provides the capability to rapidly quantify cell concentration within 3-D tissue constructs noninvasively and nondestructively. PMID:24627179

  8. 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.

  9. A quantitative structure--activity relationship model for the intrinsic activity of uncouplers of oxidative phosphorylation.

    PubMed

    Spycher, Simon; Escher, Beate I; Gasteiger, Johann

    2005-12-01

    A quantitative structure-activity relationship (QSAR) has been derived for the prediction of the activity of phenols in uncoupling oxidative and photophosphorylation. Twenty-one compounds with experimental data for uncoupling activity as well as for the acid dissociation constant, pKa, and for partitioning constants of the neutral and the charged species into model membranes were analyzed. From these measured data, the effective concentration in the membrane was derived, which allowed the study of the intrinsic activity of uncouplers within the membrane. A linear regression model for the intrinsic activity could be established using the following three descriptors: solvation free energies of the anions, an estimate for heterodimer formation describing transport processes, and pKa values describing the speciation of the phenols. In a next step, the aqueous effect concentrations were modeled by combining the model for the intrinsic uncoupling activity with descriptors accounting for the uptake into membranes. Results obtained with experimental membrane-water partitioning data were compared with the results obtained with experimental octanol-water partition coefficients, log Kow, and with calculated log Kow values. The properties of these different measures of lipophilicity were critically discussed. PMID:16359176

  10. Poisson Parameters of Antimicrobial Activity: A Quantitative Structure-Activity Approach

    PubMed Central

    Sestraş, Radu E.; Jäntschi, Lorentz; Bolboacă, Sorana D.

    2012-01-01

    A contingency of observed antimicrobial activities measured for several compounds vs. a series of bacteria was analyzed. A factor analysis revealed the existence of a certain probability distribution function of the antimicrobial activity. A quantitative structure-activity relationship analysis for the overall antimicrobial ability was conducted using the population statistics associated with identified probability distribution function. The antimicrobial activity proved to follow the Poisson distribution if just one factor varies (such as chemical compound or bacteria). The Poisson parameter estimating antimicrobial effect, giving both mean and variance of the antimicrobial activity, was used to develop structure-activity models describing the effect of compounds on bacteria and fungi species. Two approaches were employed to obtain the models, and for every approach, a model was selected, further investigated and found to be statistically significant. The best predictive model for antimicrobial effect on bacteria and fungi species was identified using graphical representation of observed vs. calculated values as well as several predictive power parameters. PMID:22606039

  11. Quantitation of proteinuria in nephrotic syndrome by spot urine protein creatinine ratio estimation in children.

    PubMed

    Biswas, A; Kumar, R; Chaterjee, A; Ghosh, J K; Basu, K

    2009-01-01

    In Nephrotic Syndrome the amount of protein excretion is a reflection of activity of disease. Quantitative measurement of proteinuria by a 24-hour urine collection has been the accepted method of evaluation. Recent studies have shown that calculation of protein/creatinine ratio in a spot urine sample correlates well with the 24-hour urine protein (24-HUP) excretion. A study was conducted to compare the accuracy of a spot urinary protein/creatinine ratio (P/C ratio) and urinary dipstick with the 24-hour urine protein. Fifty two samples from 26 patients of nephrotic syndrome were collected. This included a 24-hour urine sample followed by the next voided random spot sample. The protein/creatinine ratio was calculated and dipstick was performed on the spot sample. This was compared with the 24-hour urine protein excretion. The correlation between the three samples was statistically highly significant (p<0.001) for all levels of proteinuria. The normal value of protein/creatinine ratio in Indian children was also estimated on 50 normal children admitted in the ward without any renal diseases calculated to be 0.053 (SE of mean+/-0.003). PMID:19182753

  12. 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

  13. A laser gyro with a four-mirror square resonator: quantitative estimation of the dependence of the synchronisation zone parameters of the frequencies of counterpropagating waves on the active-medium gain

    SciTech Connect

    Bondarenko, Evgenii A

    2012-05-31

    For a laser gyro with a four-mirror square resonator (with a perimeter of 20 cm) we have calculated, on the basis of the previously developed [see Bondarenko E.A. Quantum Electron., 41, 824 (2011)] model, the dependence of the parameters of the synchronisation zone of the frequencies of counterpropagating waves on the active-medium gain. The results obtained are in qualitative agreement with known experimental data for gyroscopes with three-mirror resonators.

  14. Quantitative observations of cavitation activity in a viscoelastic medium.

    PubMed

    Collin, Jamie R T; Coussios, Constantin C

    2011-11-01

    Quantitative experimental observations of single-bubble cavitation in viscoelastic media that would enable validation of existing models are presently lacking. In the present work, single bubble cavitation is induced in an agar gel using a 1.15 MHz high intensity focused ultrasound transducer, and observed using a focused single-element passive cavitation detection (PCD) transducer. To enable quantitative observations, a full receive calibration is carried out of a spherically focused PCD system by a bistatic scattering substitution technique that uses an embedded spherical scatterer and a hydrophone. Adjusting the simulated pressure received by the PCD by the transfer function on receive and the frequency-dependent attenuation of agar gel enables direct comparison of the measured acoustic emissions with those predicted by numerical modeling of single-bubble cavitation using a modified Keller-Miksis approach that accounts for viscoelasticity of the surrounding medium. At an incident peak rarefactional pressure near the cavitation threshold, period multiplying is observed in both experiment and numerical model. By comparing the two sets of results, an estimate of the equilibrium bubble radius in the experimental observations can be made, with potential for extension to material parameter estimation. Use of these estimates yields good agreement between model and experiment. PMID:22088001

  15. 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

  16. 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.

  17. Quantitative precipitation estimation by merging multiple precipitation products using artificial neural networks

    NASA Astrophysics Data System (ADS)

    Chiang, Y.; Tsai, M.; Chang, F.

    2010-12-01

    Simulation of extreme rainfall-runoff events is the key issue for flood mitigation. The accuracy of flood forecasting driven from models is usually dependent on whether the upstream precipitation information is sufficient or not. In the past, such information was provided by ground measurements. However, remote sensing data such as radar and satellite images have been widely applied to precipitation estimation in recent years. The development of remotely sensed technology enables researchers to realize the spatial distribution of rainfall. As far as quantitative precipitation estimation is concerned, remote sensing data provide more useful information than ground measurements. It will have potential advantage of reducing the flood risk if ground observations and radar and satellite estimations can be appropriately integrated. Therefore, we first analyze the long-term variation and the correlation between observations and different products by statistical methods in this study. Secondly, the observational/ estimated errors of different precipitation sources are investigated and the biases of each precipitation products are removed by artificial neural networks. Finally, accurate quantitative precipitation estimation can be built by integrating different precipitation products.

  18. 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

  19. The quantitative estimation of the vulnerability of brick and concrete building impacted by debris flow

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Guo, Z. X.; Wang, D.; Qian, H.

    2015-08-01

    There is little historic data about the vulnerability of the damage elements in debris flow disaster in China. Therefore, it is difficult to estimate the vulnerability of debris flow quantitatively. This paper was devoted to the research of the vulnerability of brick and concrete building impacted by debris flow which widely existed in affected area. Under two assumptions, several prototype walls of brick and concrete were constructed to simulate the damaged structures in debris flow while the iron spheres were taken as the substitute of debris flow. The failure criterion of brick and concrete building was proposed with referring to the structure standards (brick and concrete) and the damage pattern in debris flow. The quantitatively estimation of vulnerability of brick and concrete building was finally established based on Fuzzy mathematics and the proposed failure criterion. The results show that the maximum impact bending moment is the best fit to be the disaster-causing factor in vulnerability curve and formula. The experiments in this paper is the preliminary research on the vulnerability of the element impacted by debris flow. The method and conclusion will be useful for the quantitative estimation of the vulnerability in debris flow and also can be referred in other types of the vulnerable elements research.

  20. 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

  1. [Method of quantitative determination of staphylococcal hyaluronidase activity].

    PubMed

    Generalov, I I

    1998-03-01

    The proposed method for measuring hyaluronidase activity of microorganism is based on prevention of hyaluronic acid clot formation with rivanol under the effect of hyaluronidase. This made possible the quantitative and qualitative detection of hyaluronidase activities of different staphylococcus species and strains. The maximum level of the enzyme and highest rate of its detection were typical of St. aureus. Its strains producing hyaluronidase in quantities of at least 0.5 IU are significantly (p < 0.01) more often isolated from medical staff. PMID:9575732

  2. Activity estimation in radioimmunotherapy using magnetic nanoparticles

    PubMed Central

    Rajabi, Hossein; Johari Daha, Fariba

    2015-01-01

    Objective Estimation of activity accumulated in tumor and organs is very important in predicting the response of radiopharmaceuticals treatment. In this study, we synthesized 177Lutetium (177Lu)-trastuzumab-iron oxide nanoparticles as a double radiopharmaceutical agent for treatment and better estimation of organ activity in a new way by magnetic resonance imaging (MRI). Methods 177Lu-trastuzumab-iron oxide nanoparticles were synthesized and all the quality control tests such as labeling yield, nanoparticle size determination, stability in buffer and blood serum up to 4 d, immunoreactivity and biodistribution in normal mice were determined. In mice bearing breast tumor, liver and tumor activities were calculated with three methods: single photon emission computed tomography (SPECT), MRI and organ extraction, which were compared with each other. Results The good results of quality control tests (labeling yield: 61%±2%, mean nanoparticle hydrodynamic size: 41±15 nm, stability in buffer: 86%±5%, stability in blood serum: 80%±3%, immunoreactivity: 80%±2%) indicated that 177Lu-trastuzumab-iron oxide nanoparticles could be used as a double radiopharmaceutical agent in mice bearing tumor. Results showed that 177Lu-trastuzumab-iron oxide nanoparticles with MRI had the ability to measure organ activities more accurate than SPECT. Conclusions Co-conjugating radiopharmaceutical to MRI contrast agents such as iron oxide nanoparticles may be a good way for better dosimetry in nuclear medicine treatment. PMID:25937783

  3. 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. PMID:18361735

  4. Radar Based Probabilistic Quantitative Precipitation Estimation: First Results of Large Sample Data Analysis

    NASA Astrophysics Data System (ADS)

    Ciach, G. J.; Krajewski, W. F.; Villarini, G.

    2005-05-01

    Large uncertainties in the operational precipitation estimates produced by the U.S. national network of WSR-88D radars are well-acknowledged. However, quantitative information about these uncertainties is not operationally available. In an effort to fill this gap, the U.S. National Weather Service (NWS) is supporting the development of a probabilistic approach to the radar precipitation estimation. The probabilistic quantitative precipitation estimation (PQPE) methodology that was selected for this development is based on the empirically-based modeling of the functional-statistical error structure in the operational WSR-88D precipitation products under different conditions. Our first goal is to deliver a realistic parameterization of the probabilistic error model describing its dependences on the radar-estimated precipitation value, distance from the radar, season, spatiotemporal averaging scale, and the setup of the precipitation processing system (PPS). In the long-term perspective, when large samples of relevant data are available, we will extend the model to include the dependences on different types of precipitation estimates (e.g. polarimeteric and multi-sensor), geographic locations and climatic regimes. At this stage of the PQPE project, we organized a 6-year-long sample of the Level II data from the Oklahoma City radar station (KTLX), and processed it with the Built 4 of the PPS that is currently used in the NWS operations. This first set of operational products was generated with the standard setup of the PPS parameters. The radar estimates are completed with the corresponding raingauge data from the Oklahoma Mesonet, the ARS Little Washita Micronet and the EVAC PicoNet covering different spatial scales. The raingauge data are used as a ground reference (GR) to estimate the required uncertainty characteristics in the radar precipitation products. In this presentation, we describe the first results of the large-sample uncertainty analysis of the products

  5. 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.

  6. Partitioning and lipophilicity in quantitative structure-activity relationships.

    PubMed Central

    Dearden, J C

    1985-01-01

    The history of the relationship of biological activity to partition coefficient and related properties is briefly reviewed. The dominance of partition coefficient in quantitation of structure-activity relationships is emphasized, although the importance of other factors is also demonstrated. Various mathematical models of in vivo transport and binding are discussed; most of these involve partitioning as the primary mechanism of transport. The models describe observed quantitative structure-activity relationships (QSARs) well on the whole, confirming that partitioning is of key importance in in vivo behavior of a xenobiotic. The partition coefficient is shown to correlate with numerous other parameters representing bulk, such as molecular weight, volume and surface area, parachor and calculated indices such as molecular connectivity; this is especially so for apolar molecules, because for polar molecules lipophilicity factors into both bulk and polar or hydrogen bonding components. The relationship of partition coefficient to chromatographic parameters is discussed, and it is shown that such parameters, which are often readily obtainable experimentally, can successfully supplant partition coefficient in QSARs. The relationship of aqueous solubility with partition coefficient is examined in detail. Correlations are observed, even with solid compounds, and these can be used to predict solubility. The additive/constitutive nature of partition coefficient is discussed extensively, as are the available schemes for the calculation of partition coefficient. Finally the use of partition coefficient to provide structural information is considered. It is shown that partition coefficient can be a valuable structural tool, especially if the enthalpy and entropy of partitioning are available. PMID:3905374

  7. 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.

  8. 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.

  9. Quantitative estimation of hemorrhage in chronic subdural hematoma using the /sup 51/Cr erythrocyte labeling method

    SciTech Connect

    Ito, H.; Yamamoto, S.; Saito, K.; Ikeda, K.; Hisada, K.

    1987-06-01

    Red cell survival studies using an infusion of chromium-51-labeled erythrocytes were performed to quantitatively estimate hemorrhage in the chronic subdural hematoma cavity of 50 patients. The amount of hemorrhage was determined during craniotomy. Between 6 and 24 hours after infusion of the labeled red cells, hemorrhage accounted for a mean of 6.7% of the hematoma content, indicating continuous or intermittent hemorrhage into the cavity. The clinical state of the patients and the density of the chronic subdural hematoma on computerized tomography scans were related to the amount of hemorrhage. Chronic subdural hematomas with a greater amount of hemorrhage frequently consisted of clots rather than fluid.

  10. 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.

  11. 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.

  12. On the use of radar-based quantitative precipitation estimates for precipitation frequency analysis

    NASA Astrophysics Data System (ADS)

    Eldardiry, Hisham; Habib, Emad; Zhang, Yu

    2015-12-01

    The high spatio-temporal resolutions of radar-based multi-sensor Quantitative Precipitation Estimates (QPEs) makes them a potential complement to the gauge records for engineering design purposes, such as precipitation frequency analysis. The current study investigates three fundamental issues that arise when radar-based QPE products are used in frequency analysis: (a) Effect of sample size due to the typically short records of radar products; (b) Effect of uncertainties present in radar-rainfall estimation algorithms; and (c) Effect of the frequency estimation approach adopted. The study uses a 13-year dataset of hourly, 4 × 4 km2 radar-based over a domain that covers Louisiana, USA. Data-based investigations, as well as synthetic simulations, are performed to quantify the uncertainties associated with the radar-based derived frequencies, and to gain insight into the relative contributions of short record lengths and those from conditional biases in the radar product. Three regional estimation procedures were tested and the results indicate the sensitivity of the radar frequency estimates to the selection of the estimation approach and the impact on the uncertainties of the derived extreme quantiles. The simulation experiments revealed that the relatively short radar records explained the majority of the uncertainty associated with the radar-based quantiles; however, they did not account for any tangible contribution to the systematic underestimation observed between radar- and gauge-based frequency estimates. This underestimation was mostly attributable to the conditional bias inherent in the radar product. Addressing such key outstanding problems in radar-rainfall products is necessary before they can be fully and reliably used for frequency analysis applications.

  13. Estimation of the number of fluorescent end-members for quantitative analysis of multispectral FLIM data

    PubMed Central

    Gutierrez-Navarro, Omar; Campos-Delgado, Daniel U.; Arce-Santana, Edgar R.; Maitland, Kristen C.; Cheng, Shuna; Jabbour, Joey; Malik, Bilal; Cuenca, Rodrigo; Jo, Javier A.

    2014-01-01

    Multispectral fluorescence lifetime imaging (m-FLIM) can potentially allow identifying the endogenous fluorophores present in biological tissue. Quantitative description of such data requires estimating the number of components in the sample, their characteristic fluorescent decays, and their relative contributions or abundances. Unfortunately, this inverse problem usually requires prior knowledge about the data, which is seldom available in biomedical applications. This work presents a new methodology to estimate the number of potential endogenous fluorophores present in biological tissue samples from time-domain m-FLIM data. Furthermore, a completely blind linear unmixing algorithm is proposed. The method was validated using both synthetic and experimental m-FLIM data. The experimental m-FLIM data include in-vivo measurements from healthy and cancerous hamster cheek-pouch epithelial tissue, and ex-vivo measurements from human coronary atherosclerotic plaques. The analysis of m-FLIM data from in-vivo hamster oral mucosa identified healthy from precancerous lesions, based on the relative concentration of their characteristic fluorophores. The algorithm also provided a better description of atherosclerotic plaques in term of their endogenous fluorophores. These results demonstrate the potential of this methodology to provide quantitative description of tissue biochemical composition. PMID:24921344

  14. The quantitative estimation of the vulnerability of brick and concrete wall impacted by an experimental boulder

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Guo, Z. X.; Wang, D.; Qian, H.

    2016-02-01

    There is little historic data about the vulnerability of damaged elements due to debris flow events in China. Therefore, it is difficult to quantitatively estimate the vulnerable elements suffered by debris flows. This paper is devoted to the research of the vulnerability of brick and concrete walls impacted by debris flows. An experimental boulder (an iron sphere) was applied to be the substitute of debris flow since it can produce similar shape impulse load on elements as debris flow. Several walls made of brick and concrete were constructed in prototype dimensions to physically simulate the damaged structures in debris flows. The maximum impact force was measured, and the damage conditions of the elements (including cracks and displacements) were collected, described and compared. The failure criterion of brick and concrete wall was proposed with reference to the structure characteristics as well as the damage pattern caused by debris flows. The quantitative estimation of the vulnerability of brick and concrete wall was finally established based on fuzzy mathematics and the proposed failure criterion. Momentum, maximum impact force and maximum impact bending moment were compared to be the best candidate for disaster intensity index. The results show that the maximum impact bending moment seems to be most suitable for the disaster intensity index in establishing vulnerability curve and formula.

  15. 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.

  16. 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.

  17. Estimating effects of a single gene and polygenes on quantitative traits from a diallel design.

    PubMed

    Lou, Xiang-Yang; Yang, Mark C K

    2006-01-01

    A genetic model is developed with additive and dominance effects of a single gene and polygenes as well as general and specific reciprocal effects for the progeny from a diallel mating design. The methods of ANOVA, minimum norm quadratic unbiased estimation (MINQUE), restricted maximum likelihood estimation (REML), and maximum likelihood estimation (ML) are suggested for estimating variance components, and the methods of generalized least squares (GLS) and ordinary least squares (OLS) for fixed effects, while best linear unbiased prediction, linear unbiased prediction (LUP), and adjusted unbiased prediction are suggested for analyzing random effects. Monte Carlo simulations were conducted to evaluate the unbiasedness and efficiency of statistical methods involving two diallel designs with commonly used sample sizes, 6 and 8 parents, with no and missing crosses, respectively. Simulation results show that GLS and OLS are almost equally efficient for estimation of fixed effects, while MINQUE (1) and REML are better estimators of the variance components and LUP is most practical method for prediction of random effects. Data from a Drosophila melanogaster experiment (Gilbert 1985a, Theor appl Genet 69:625-629) were used as a working example to demonstrate the statistical analysis. The new methodology is also applicable to screening candidate gene(s) and to other mating designs with multiple parents, such as nested (NC Design I) and factorial (NC Design II) designs. Moreover, this methodology can serve as a guide to develop new methods for detecting indiscernible major genes and mapping quantitative trait loci based on mixture distribution theory. The computer program for the methods suggested in this article is freely available from the authors. PMID:17028974

  18. 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

  19. 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

  20. 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

  1. 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.

  2. Uncertainties in Surface Runoff Forecasts Driven by Probabilistic Quantitative Precipitation Estimates

    NASA Astrophysics Data System (ADS)

    Ntelekos, A. A.; Ciach, G. J.; Georgakakos, K. P.; Krajewski, W. F.

    2004-05-01

    This work focuses on several aspects of the ensemble flood forecasting with the embedded input and model uncertainties. In most of the short term forecasting, hydrologic models apply the input rainfall estimates assuming that they are error-free. For example, this is the case with the operational use of the Sacramento--Soil Moisture Accounting (SAC-SMA) model at the US National Weather Service (NWS) River Forecast Centers (RFC's). We apply an analytical approximation of the upper soil zone equations in the SAC-SMA model to study the propagation of the uncertainties in rainfall estimates into runoff generation. The ensembles of the rainfall estimates are produced by randomizing the radar-rainfall arrays costructed from the WSR-88D data. These ensembles are the specific outcomes of a general probabilistic quantitative precipitation estimation (PQPE) procedure currently developed by the University of Iowa for the NWS. The parameters of the rainfall uncertainty generator describe the conditional distributions of the error process and its spatiotemporal dependences. This investigation is performed using two different uncertainty schemes. In the first scenario, only the errors in rainfall estimates are assumed. Here, the parameter values of the SAC-SMA model are fixed and based on the data from a watershed located within the Illinois River basin in Oklahoma. In the second scenario, nominal uncertainties in the SAC-SMA model parameters are added. Our study aims to identify those characteristics of the radar-rainfall error process that are mostly responsible for the uncertainty in surface runoff production by the operational hydrologic models.

  3. Using Extended Genealogy to Estimate Components of Heritability for 23 Quantitative and Dichotomous Traits

    PubMed Central

    Zaitlen, Noah; Kraft, Peter; Patterson, Nick; Pasaniuc, Bogdan; Bhatia, Gaurav; Pollack, Samuela; Price, Alkes L.

    2013-01-01

    Important knowledge about the determinants of complex human phenotypes can be obtained from the estimation of heritability, the fraction of phenotypic variation in a population that is determined by genetic factors. Here, we make use of extensive phenotype data in Iceland, long-range phased genotypes, and a population-wide genealogical database to examine the heritability of 11 quantitative and 12 dichotomous phenotypes in a sample of 38,167 individuals. Most previous estimates of heritability are derived from family-based approaches such as twin studies, which may be biased upwards by epistatic interactions or shared environment. Our estimates of heritability, based on both closely and distantly related pairs of individuals, are significantly lower than those from previous studies. We examine phenotypic correlations across a range of relationships, from siblings to first cousins, and find that the excess phenotypic correlation in these related individuals is predominantly due to shared environment as opposed to dominance or epistasis. We also develop a new method to jointly estimate narrow-sense heritability and the heritability explained by genotyped SNPs. Unlike existing methods, this approach permits the use of information from both closely and distantly related pairs of individuals, thereby reducing the variance of estimates of heritability explained by genotyped SNPs while preventing upward bias. Our results show that common SNPs explain a larger proportion of the heritability than previously thought, with SNPs present on Illumina 300K genotyping arrays explaining more than half of the heritability for the 23 phenotypes examined in this study. Much of the remaining heritability is likely to be due to rare alleles that are not captured by standard genotyping arrays. PMID:23737753

  4. 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

  5. Quantitative estimation of surface ocean productivity and bottom water oxygen concentration using benthic foraminifera

    NASA Astrophysics Data System (ADS)

    Loubere, Paul

    1994-10-01

    An electronic supplement of this material may be obtained on adiskette or Anonymous FTP from KOSMOS.AGU.ORG. (LOGIN toAGU's FTP account using ANONYMOUS as the usemame andGUEST as the password. Go to the right directory by typing CDAPEND. Type LS to see what files are available. Type GET and thename of the file to get it. Finally, type EXIT to leave the system.)(Paper 94PA01624, Quantitative estimation of surface oceanproductivity and bottom water concentration using benthicforaminifera, by P. Loubere). Diskette may be ordered from AmericanGeophysical Union, 2000 Florida Avenue, N.W., Washington, DC20009; $15.00. Payment must accompany order.Quantitative estimation of surface ocean productivity and bottom water oxygen concentration with benthic foraminifera was attempted using 70 samples from equatorial and North Pacific surface sediments. These samples come from a well defined depth range in the ocean, between 2200 and 3200 m, so that depth related factors do not interfere with the estimation. Samples were selected so that foraminifera were well preserved in the sediments and temperature and salinity were nearly uniform (T = 1.5° C; S = 34.6‰). The sample set was also assembled so as to minimize the correlation often seen between surface ocean productivity and bottom water oxygen values (r² = 0.23 for prediction purposes in this case). This procedure reduced the chances of spurious results due to correlations between the environmental variables. The samples encompass a range of productivities from about 25 to >300 gC m-2 yr-1, and a bottom water oxygen range from 1.8 to 3.5 ml/L. Benthic foraminiferal assemblages were quantified using the >62 µm fraction of the sediments and 46 taxon categories. MANOVA multivariate regression was used to project the faunal matrix onto the two environmental dimensions using published values for productivity and bottom water oxygen to calibrate this operation. The success of this regression was measured with the multivariate r

  6. Quantitative Functional Imaging Using Dynamic Positron Computed Tomography and Rapid Parameter Estimation Techniques

    NASA Astrophysics Data System (ADS)

    Koeppe, Robert Allen

    Positron computed tomography (PCT) is a diagnostic imaging technique that provides both three dimensional imaging capability and quantitative measurements of local tissue radioactivity concentrations in vivo. This allows the development of non-invasive methods that employ the principles of tracer kinetics for determining physiological properties such as mass specific blood flow, tissue pH, and rates of substrate transport or utilization. A physiologically based, two-compartment tracer kinetic model was derived to mathematically describe the exchange of a radioindicator between blood and tissue. The model was adapted for use with dynamic sequences of data acquired with a positron tomograph. Rapid estimation techniques were implemented to produce functional images of the model parameters by analyzing each individual pixel sequence of the image data. A detailed analysis of the performance characteristics of three different parameter estimation schemes was performed. The analysis included examination of errors caused by statistical uncertainties in the measured data, errors in the timing of the data, and errors caused by violation of various assumptions of the tracer kinetic model. Two specific radioindicators were investigated. ('18)F -fluoromethane, an inert freely diffusible gas, was used for local quantitative determinations of both cerebral blood flow and tissue:blood partition coefficient. A method was developed that did not require direct sampling of arterial blood for the absolute scaling of flow values. The arterial input concentration time course was obtained by assuming that the alveolar or end-tidal expired breath radioactivity concentration is proportional to the arterial blood concentration. The scale of the input function was obtained from a series of venous blood concentration measurements. The method of absolute scaling using venous samples was validated in four studies, performed on normal volunteers, in which directly measured arterial concentrations

  7. Evaluation of a rapid method for the quantitative estimation of coliforms in meat by impedimetric procedures.

    PubMed Central

    Martins, S B; Selby, M J

    1980-01-01

    A 24-h instrumental procedure is described for the quantitative estimation of coliforms in ground meat. The method is simple and rapid, and it requires but a single sample dilution and four replicates. The data are recorded automatically and can be used to estimate coliforms in the range of 100 to 10,000 organisms per g. The procedure is an impedance detection time (IDT) method using a new medium, tested against 131 stock cultures, that markedly enhances the impedance response of gram-negative organisms, and it is selective for coliforms. Seventy samples of ground beef were analyzed for coliforms by the IDT method and the conventional three-dilution, two-step most-probable-number test tube procedure. Seventy-nine percent of the impedimetric estimates fell within the 95% confidence limits of the most-probable-number values. This corresponds to the criteria used to evaluate other coliform tests, with the added advantage of a single dilution and more rapid results. PMID:6992712

  8. 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.

  9. 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

  10. 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

  11. Quantitative phase imaging technologies to assess neuronal activity (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Thouvenin, Olivier; Fink, Mathias; Boccara, Claude

    2016-03-01

    Active neurons tends to have a different dynamical behavior compared to resting ones. Non-exhaustively, vesicular transport towards the synapses is increased, since axonal growth becomes slower. Previous studies also reported small phase variations occurring simultaneously with the action potential. Such changes exhibit times scales ranging from milliseconds to several seconds on spatial scales smaller than the optical diffraction limit. Therefore, QPI systems are of particular interest to measure neuronal activity without labels. Here, we report the development of two new QPI systems that should enable the detection of such activity. Both systems can acquire full field phase images with a sub nanometer sensitivity at a few hundreds of frames per second. The first setup is a synchronous combination of Full Field Optical Coherence Tomography (FF-OCT) and Fluorescence wide field imaging. The latter modality enables the measurement of neurons electrical activity using calcium indicators. In cultures, FF-OCT exhibits similar features to Digital Holographic Microscopy (DHM), except from complex computational reconstruction. However, FF-OCT is of particular interest in order to measure phase variations in tissues. The second setup is based on a Quantitative Differential Interference Contrast setup mounted in an epi-illumination configuration with a spectrally incoherent illumination. Such a common path interferometer exhibits a very good mechanical stability, and thus enables the measurement of phase images during hours. Additionally, such setup can not only measure a height change, but also an optical index change for both polarization. Hence, one can measure simultaneously a phase change and a birefringence change.

  12. A quantitative method for estimation of volume changes in arachnoid foveae with age.

    PubMed

    Duray, Stephen M; Martel, Stacie S

    2006-03-01

    Age-related changes of arachnoid foveae have been described, but objective, quantitative analyses are lacking. A new quantitative method is presented for estimation of change in total volume of arachnoid foveae with age. The pilot sample consisted of nine skulls from the Palmer Anatomy Laboratory. Arachnoid foveae were filled with sand, which was extracted using a vacuum pump. Mass was determined with an analytical balance and converted to volume. A reliability analysis was performed using intraclass correlation coefficients. The method was found to be highly reliable (intraobserver ICC = 0.9935, interobserver ICC = 0.9878). The relationship between total volume and age was then examined in a sample of 63 males of accurately known age from the Hamann-Todd collection. Linear regression analysis revealed no statistically significant relationship between total volume and age, or foveae frequency and age (alpha = 0.05). Development of arachnoid foveae may be influenced by health factors, which could limit its usefulness in aging. PMID:16566755

  13. 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. PMID:24658719

  14. 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

  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. PMID:19587415

  16. 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).

  17. 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.

  18. 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. PMID:26890190

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. Quantitative analysis of wrist electrodermal activity during sleep.

    PubMed

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

    2014-12-01

    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 the 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 1960s, we systematically compare thresholds for automatically detecting EDA peaks and establish criteria for EDA storms. We found that more than 80% of the 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 to occur 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

  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. A quantitative estimation of the energetic cost of brown ring disease in the Manila clam using Dynamic Energy Budget theory

    NASA Astrophysics Data System (ADS)

    Flye-Sainte-Marie, Jonathan; Jean, Fred; Paillard, Christine; Kooijman, Sebastiaan A. L. M.

    2009-08-01

    Brown ring disease (BRD) in the Manila clam, Ruditapes philippinarum, is a bacterial disease caused by the pathogen Vibrio tapetis. This disease induces the formation of a characteristic brown conchiolin deposit on the inner shell and is associated with a decrease in condition index indicating that the development of the disease affects the energy balance of the clam. A previous study showed that the energy budget of the host was affected by a decrease in filtration activity, and hypothesized that a second way to degrade the energy balance was the increase in maintenance costs associated to the cost of immune response and lesion repair. This paper focusses on this second way of degradation of the energy balance. A starvation experiment confirmed that the energy balance was affected by BRD, independently of the effects on filtration activity, indicating an increase in the maintenance costs. An energy budget model of the Manila clam, based on DEB theory, was developed and allowed to properly predict weight loss during starvation. Vibrio development and its effects on the energy budget of the host was theoretically introduced in the model. Coupling modelling and experimental observations allowed to provide a quantitative and dynamic estimation of the increase in maintenance costs associated with the development of BRD. The estimation which is given here, indicates that during an infection the maintenance cost can almost double compared to the uninfected situation. Further development of the model, especially focussed on Vibrio dynamics and its effects on filtration activity is needed to provide a more extensive description of the energetic cost of BRD in the Manila clam.

  9. 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

  10. Estimation of the patient monitor alarm rate for a quantitative analysis of new alarm settings.

    PubMed

    de Waele, Stijn; Nielsen, Larry; Frassica, Joseph

    2014-01-01

    In many critical care units, default patient monitor alarm settings are not fine-tuned to the vital signs of the patient population. As a consequence there are many alarms. A large fraction of the alarms are not clinically actionable, thus contributing to alarm fatigue. Recent attention to this phenomenon has resulted in attempts in many institutions to decrease the overall alarm load of clinicians by altering the trigger thresholds for monitored parameters. Typically, new alarm settings are defined based on clinical knowledge and patient population norms and tried empirically on new patients without quantitative knowledge about the potential impact of these new settings. We introduce alarm regeneration as a method to estimate the alarm rate of new alarm settings using recorded patient monitor data. This method enables evaluation of several alarm setting scenarios prior to using these settings in the clinical setting. An expression for the alarm rate variance is derived for the calculation of statistical confidence intervals on the results. PMID:25571296

  11. Quantitative and Rapid Estimation of H+ Fluxes in Membrane Vesicles 1

    PubMed Central

    Jennings, Ian R.; Rea, Philip A.; Leigh, Roger A.; Sanders, Dale

    1988-01-01

    Proton transport is often visualized in membrane vesicles by use of fluorescent monoamines which accumulate in acidic intravesicular compartments and undergo concentration-dependent fluorescence quenching. Software for an IBM microcomputer is described which permits logging and editing of changes in fluorescence monitored by a Perkin-Elmer LS-5 luminescence spectrometer. An accurate estimate of the instantaneous rate of fluorescence quenching or recovery is then facilitated by least squares fitting of fluorescence data to a nonlinear function. The software is tested with tonoplast vesicles from Beta vulgaris. Quenching of acridine orange fluorescence by ATP-driven (primary) transport and relaxation of quenching by Na+/H+ antiport can both be fitted with single exponential functions. Initial rates of ATP- and Na+ -dependent fluorescence changes are derived and can be used for Km determinations. The method constitutes a simple and efficient alternative to manual analysis of analog fluorescence traces and results in a reliable quantitative measurement of the relative rate of proton transport in membrane vesicle preparations. PMID:16666064

  12. 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

  13. 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.

  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

    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. 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

  17. 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.

  18. Using Modified Contour Deformable Model to Quantitatively Estimate Ultrasound Parameters for Osteoporosis Assessment

    NASA Astrophysics Data System (ADS)

    Chen, Yung-Fu; Du, Yi-Chun; Tsai, Yi-Ting; Chen, Tainsong

    Osteoporosis is a systemic skeletal disease, which is characterized by low bone mass and micro-architectural deterioration of bone tissue, leading to bone fragility. Finding an effective method for prevention and early diagnosis of the disease is very important. Several parameters, including broadband ultrasound attenuation (BUA), speed of sound (SOS), and stiffness index (STI), have been used to measure the characteristics of bone tissues. In this paper, we proposed a method, namely modified contour deformable model (MCDM), bases on the active contour model (ACM) and active shape model (ASM) for automatically detecting the calcaneus contour from quantitative ultrasound (QUS) parametric images. The results show that the difference between the contours detected by the MCDM and the true boundary for the phantom is less than one pixel. By comparing the phantom ROIs, significant relationship was found between contour mean and bone mineral density (BMD) with R=0.99. The influence of selecting different ROI diameters (12, 14, 16 and 18 mm) and different region-selecting methods, including fixed region (ROI fix ), automatic circular region (ROI cir ) and calcaneal contour region (ROI anat ), were evaluated for testing human subjects. Measurements with large ROI diameters, especially using fixed region, result in high position errors (10-45%). The precision errors of the measured ultrasonic parameters for ROI anat are smaller than ROI fix and ROI cir . In conclusion, ROI anat provides more accurate measurement of ultrasonic parameters for the evaluation of osteoporosis and is useful for clinical application.

  19. 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. PMID:26085428

  20. 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

  1. 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)

  2. 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

  3. Estimates of activation in arterial smooth muscle.

    PubMed

    Singer, H A; Kamm, K E; Murphy, R A

    1986-09-01

    We have previously described the onset of a "latch" state in the swine carotid media after K+ depolarization. This state was characterized by maintained stress after a decrease in shortening velocities and in the level of cross-bridge phosphorylation. The present experiments were designed to determine whether there were changes in other mechanical properties in swine carotid media associated with the onset of the latch state. Medial strips (less than 500 microM thick), incubated in physiological salt solution (PSS) at 37 degrees C at their optimal length (Lo), were subjected to ramp stretches (5.86 mm/s) of 5% Lo. The active stress (Sa) response to stretch was computed by subtraction of the passive element contribution (as determined from identical stretches after 30 min incubation in Ca2+-free PSS) from the total response in the activated muscle. Transitions in the total and active stress responses to stretch were observed in strips stimulated with 109 mM K+ for 1 min or longer and were interpreted as yielding of the contractile apparatus. Active dynamic stiffness (dS/dLo) calculated from the initial 1% Lo portion of the stretch response, correlated linearly with active stress over a wide range. Maximal stress and dynamic stiffness were reached by 1 min and were maintained for at least 30 min in K+-depolarized preparations. However, yield stress increased significantly between 1 and 10 min, and there was a large increase in the length at which yield was observed (1.09 +/- 0.06 to 1.86 +/- 0.10% Lo; n = 9). These increases were maintained between 10 and 30 min.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:3752237

  4. Quantitative Packaging of Active Enzymes into a Protein Cage.

    PubMed

    Azuma, Yusuke; Zschoche, Reinhard; Tinzl, Matthias; Hilvert, Donald

    2016-01-22

    Genetic fusion of cargo proteins to a positively supercharged variant of green fluorescent protein enables their quantitative encapsulation by engineered lumazine synthase capsids possessing a negatively charged lumenal surface. This simple tagging system provides a robust and versatile means of creating hierarchically ordered protein assemblies for use as nanoreactors. The generality of the encapsulation strategy and its effect on enzyme function were investigated with eight structurally and mechanistically distinct catalysts. PMID:26695342

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. 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…

  11. 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. PMID:26269460

  12. 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

  13. 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

    2015-01-01

    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. PMID:25985362

  14. 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).

  15. 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

  16. 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.

  17. 76 FR 9637 - Proposed Information Collection (Veteran Suicide Prevention Online Quantitative Surveys) Activity...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-18

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF VETERANS AFFAIRS Proposed Information Collection (Veteran Suicide Prevention Online Quantitative Surveys) Activity... the comment period, comments may be viewed online through FDMS. FOR FURTHER INFORMATION...

  18. 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...

  19. 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...

  20. Teratogenic potency of valproate analogues evaluated by quantitative estimation of cellular morphology in vitro.

    PubMed

    Berezin, V; Kawa, A; Bojic, U; Foley, A; Nau, H; Regan, C; Edvardsen, K; Bock, E

    1996-10-01

    To develop a simple prescreening system for teratogenicity testing, a novel in vitro assay was established using computer assisted microscopy allowing automatic delineation of contours of stained cells and thereby quantitative determination of cellular morphology. The effects of valproic acid (VPA) and analogues with high as well as low teratogenic activities-(as previously determined in vivo)-were used as probes for study of the discrimination power of the in vitro model. VPA, a teratogenic analogue (+/-)-4-en-VPA, and a non-teratogenic analogue (E)-2-en-VPA, as well as the purified (S)- and (R)-enantiomers of 4-yn-VPA (teratogenic and non-teratogenic, respectively), were tested for their effects on cellular morphology of cloned mouse fibroblastoid L-cell lines, neuroblastoma N2a cells, and rat glioma BT4Cn cells, and were found to induce varying increases in cellular area: Furthermore, it was demonstrated that under the chosen conditions the increase in area correlated statistically significantly with the teratogenic potency of the employed compounds. Setting the cellular area of mouse L-cells to 100% under control conditions, the most pronounced effect was observed for (S)-4-yn-VPA (211%, P = < 0.001) followed by VPA (186%, P < 0.001), 4-en-VPA (169%, P < 0.001) and non-teratogenic 2-en-VPA (137%, P < 0.005) and (R)-4-yn-VPA (105%). This effect was independent of the choice of substrata, since it was observed on L-cells grown on plastic, fibronectin, laminin and Matrigel. However, when VPA-treated cells were exposed to an arginyl-glycyl-aspartate (RGD)-containing peptide to test whether VPA treatment was able to modulate RGD-dependent integrin interactions with components of the extracellular matrix, hardly any effect could be observed, whereas control cells readily detached from the substratum, indicating a changed substrate adhesion of the VPA-treated cells. The data thus indicate that measurement of cellular area may serve as a simple in vitro test in the

  1. Quantitative optical coherence tomography by maximum a-posteriori estimation of signal intensity

    NASA Astrophysics Data System (ADS)

    Chan, Aaron C.; Kurokawa, Kazuhiro; Makita, Shuichi; Hong, Young-Joo; Miyazawa, Arata; Miura, Masahiro; Yasuno, Yoshiaki

    2016-03-01

    A maximum a-posteriori (MAP) estimator for signal amplitude of optical coherence tomography (OCT) is presented. This estimator provides an accurate and low bias estimation of the correct OCT signal amplitude even at very low signal-tonoise ratios. As a result, contrast improvement of retinal OCT images is demonstrated. In addition, this estimation method allows for an estimation reliability to be calculated. By combining the MAP estimator with a previously demonstrated attenuation imaging algorithm, we present attenuation coefficient images of the retina. From the reliability derived from the MAP image one can also determine which regions of the attenuation images are unreliable. From Jones matrix OCT data of the optic nerve head (ONH), we also demonstrate that combining MAP with polarization diversity (PD) OCT images can generate intensity images with fewer birefringence artifacts, resulting in better attenuation images. Analysis of the MAP intensity images shows higher image SNR than averaging.

  2. 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

  3. 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…

  4. 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...

  5. 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…

  6. Improved activity estimation with MC-JOSEM versus TEW-JOSEM in 111In SPECT

    PubMed Central

    Ouyang, Jinsong; Fakhri, Georges El; Moore, Stephen C.

    2008-01-01

    We have previously developed a fast Monte Carlo (MC)-based joint ordered-subset expectation maximization (JOSEM) iterative reconstruction algorithm, MC-JOSEM. A phantom study was performed to compare quantitative imaging performance of MC-JOSEM with that of a triple-energy-window approach (TEW) in which estimated scatter was also included additively within JOSEM, TEW-JOSEM. We acquired high-count projections of a 5.5 cm3 sphere of 111In at different locations in the water-filled torso phantom; high-count projections were then obtained with 111In only in the liver or only in the soft-tissue background compartment, so that we could generate synthetic projections for spheres surrounded by various activity distributions. MC scatter estimates used by MC-JOSEM were computed once after five iterations of TEW-JOSEM. Images of different combinations of liver∕background and sphere∕background activity concentration ratios were reconstructed by both TEW-JOSEM and MC-JOSEM for 40 iterations. For activity estimation in the sphere, MC-JOSEM always produced better relative bias and relative standard deviation than TEW-JOSEM for each sphere location, iteration number, and activity combination. The average relative bias of activity estimates in the sphere for MC-JOSEM after 40 iterations was −6.9%, versus −15.8% for TEW-JOSEM, while the average relative standard deviation of the sphere activity estimates was 16.1% for MC-JOSEM, versus 27.4% for TEW-JOSEM. Additionally, the average relative bias of activity concentration estimates in the liver and the background for MC-JOSEM after 40 iterations was −3.9%, versus −12.2% for TEW-JOSEM, while the average relative standard deviation of these estimates was 2.5% for MC-JOSEM, versus 3.4% for TEW-JOSEM. MC-JOSEM is a promising approach for quantitative activity estimation in 111In SPECT. PMID:18561679

  7. Estimating ROI activity concentration with photon-processing and photon-counting SPECT imaging systems

    NASA Astrophysics Data System (ADS)

    Jha, Abhinav K.; Frey, Eric C.

    2015-03-01

    Recently a new class of imaging systems, referred to as photon-processing (PP) systems, are being developed that uses real-time maximum-likelihood (ML) methods to estimate multiple attributes per detected photon and store these attributes in a list format. PP systems could have a number of potential advantages compared to systems that bin photons based on attributes such as energy, projection angle, and position, referred to as photon-counting (PC) systems. For example, PP systems do not suffer from binning-related information loss and provide the potential to extract information from attributes such as energy deposited by the detected photon. To quantify the effects of this advantage on task performance, objective evaluation studies are required. We performed this study in the context of quantitative 2-dimensional single-photon emission computed tomography (SPECT) imaging with the end task of estimating the mean activity concentration within a region of interest (ROI). We first theoretically outline the effect of null space on estimating the mean activity concentration, and argue that due to this effect, PP systems could have better estimation performance compared to PC systems with noise-free data. To evaluate the performance of PP and PC systems with noisy data, we developed a singular value decomposition (SVD)-based analytic method to estimate the activity concentration from PP systems. Using simulations, we studied the accuracy and precision of this technique in estimating the activity concentration. We used this framework to objectively compare PP and PC systems on the activity concentration estimation task. We investigated the effects of varying the size of the ROI and varying the number of bins for the attribute corresponding to the angular orientation of the detector in a continuously rotating SPECT system. The results indicate that in several cases, PP systems offer improved estimation performance compared to PC systems.

  8. [Estimation of quantitative proteinuria using a new dipstick in random urine samples].

    PubMed

    Morishita, Yoshiyuki; Kusano, Eiji; Umino, Tetsuo; Nemoto, Jun; Tanba, Kaichirou; Ando, Yasuhiro; Muto, Shigeaki; Asano, Yasushi

    2004-02-01

    Proteinuria is quantified for diagnostic and prognostic purposes and to assess responses to therapy. Methods used to assess urinary protein include 24-hour urine collection (24-Up) and determination of the ratio of protein to creatinine concentration (Up/Ucr) in simple voided urine samples (Up/Ucr quantitative method). However, these methods are costly and time consuming. The Multistix PRO 11 (Bayer Medical Co., Ltd., Tokyo, Japan) is a new urine dipstick that allows rapid measurement of Up/Ucr. Results obtained with the Multistix PRO 11 coincided well with those obtained with the 24-Up method (kappa = 0.68) and the Up/Ucr quantitative method (kappa = 0.75). However, Multistix PRO 11 did not accurately measure moderate to severe proteinuria (> or = 500 mg/g. Cr). Our findings suggest that Multistix PRO 11 is useful for the screening, assessment, and follow-up of mild proteinuria. PMID:15058105

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

    PubMed

    St Charles, Frank Kelley; McAughey, John; Shepperd, Christopher J

    2013-06-01

    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

  10. 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

  11. A biphasic parameter estimation method for quantitative analysis of dynamic renal scintigraphic data

    NASA Astrophysics Data System (ADS)

    Koh, T. S.; Zhang, Jeff L.; Ong, C. K.; Shuter, B.

    2006-06-01

    Dynamic renal scintigraphy is an established method in nuclear medicine, commonly used for the assessment of renal function. In this paper, a biphasic model fitting method is proposed for simultaneous estimation of both vascular and parenchymal parameters from renal scintigraphic data. These parameters include the renal plasma flow, vascular and parenchymal mean transit times, and the glomerular extraction rate. Monte Carlo simulation was used to evaluate the stability and confidence of the parameter estimates obtained by the proposed biphasic method, before applying the method on actual patient study cases to compare with the conventional fitting approach and other established renal indices. The various parameter estimates obtained using the proposed method were found to be consistent with the respective pathologies of the study cases. The renal plasma flow and extraction rate estimated by the proposed method were in good agreement with those previously obtained using dynamic computed tomography and magnetic resonance imaging.

  12. Estimating base rates of impairment in neuropsychological test batteries: a comparison of quantitative models.

    PubMed

    Decker, Scott L; Schneider, W Joel; Hale, James B

    2012-01-01

    Neuropsychologists frequently rely on a battery of neuropsychological tests which are normally distributed to determine impaired functioning. The statistical likelihood of Type I error in clinical decision-making is in part determined by the base rate of normative individuals obtaining atypical performance on neuropsychological tests. Base rates are most accurately obtained by co-normed measures, but this is rarely accomplished in neuropsychological testing. Several statistical methods have been proposed to estimate base rates for tests that are not co-normed. This study compared two statistical approaches (binomial and Monte Carlo models) used to estimate the base rates for flexible test batteries. The two approaches were compared against empirically derived base rates for a multitest co-normed battery of cognitive measures. Estimates were compared across a variety of conditions including age and different α levels (N =3,356). Monte Carlo R(2) estimates ranged from .980 to .997 across five different age groups, indicating a good fit. In contrast, the binomial model fit estimates ranged from 0.387 to 0.646. Results confirm that the binomial model is insufficient for estimating base rates because it does not take into account correlations among measures in a multitest battery. Although the Monte Carlo model produced more accurate results, minor biases occurred that are likely due to skewess and kurtosis of test variables. Implications for future research and applied practice are discussed. PMID:22172567

  13. Towards a quantitative kinetic theory of polar active matter

    NASA Astrophysics Data System (ADS)

    Ihle, T.

    2014-06-01

    A recent kinetic approach for Vicsek-like models of active particles is reviewed. The theory is based on an exact Chapman- Kolmogorov equation in phase space. It can handle discrete time dynamics and "exotic" multi-particle interactions. A nonlocal mean-field theory for the one-particle distribution function is obtained by assuming molecular chaos. The Boltzmann approach of Bertin, et al., Phys. Rev. E 74, 022101 (2006) and J. Phys. A 42, 445001 (2009), is critically assessed and compared to the current approach. In Boltzmann theory, a collision starts when two particles enter each others action spheres and is finished when their distance exceeds the interaction radius. The average duration of such a collision, τ0, is measured for the Vicsek model with continuous time-evolution. If the noise is chosen to be close to the flocking threshold, the average time between collisions is found to be roughly equal to τ0 at low densities. Thus, the continuous-time Vicsek-model near the flocking threshold cannot be accurately described by a Boltzmann equation, even at very small density because collisions take so long that typically other particles join in, rendering Boltzmann's binary collision assumption invalid. Hydrodynamic equations for the phase space approach are derived by means of a Chapman-Enskog expansion. The equations are compared to the Toner-Tu theory of polar active matter. New terms, absent in the Toner-Tu theory, are highlighted. Convergence problems of Chapman-Enskog and similar gradient expansions are discussed.

  14. A quantitative analysis of contractility in active cytoskeletal protein networks.

    PubMed

    Bendix, Poul M; Koenderink, Gijsje H; Cuvelier, Damien; Dogic, Zvonimir; Koeleman, Bernard N; Brieher, William M; Field, Christine M; Mahadevan, L; Weitz, David A

    2008-04-15

    Cells actively produce contractile forces for a variety of processes including cytokinesis and motility. Contractility is known to rely on myosin II motors which convert chemical energy from ATP hydrolysis into forces on actin filaments. However, the basic physical principles of cell contractility remain poorly understood. We reconstitute contractility in a simplified model system of purified F-actin, muscle myosin II motors, and alpha-actinin cross-linkers. We show that contractility occurs above a threshold motor concentration and within a window of cross-linker concentrations. We also quantify the pore size of the bundled networks and find contractility to occur at a critical distance between the bundles. We propose a simple mechanism of contraction based on myosin filaments pulling neighboring bundles together into an aggregated structure. Observations of this reconstituted system in both bulk and low-dimensional geometries show that the contracting gels pull on and deform their surface with a contractile force of approximately 1 microN, or approximately 100 pN per F-actin bundle. Cytoplasmic extracts contracting in identical environments show a similar behavior and dependence on myosin as the reconstituted system. Our results suggest that cellular contractility can be sensitively regulated by tuning the (local) activity of molecular motors and the cross-linker density and binding affinity. PMID:18192374

  15. 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. PMID:25929827

  16. Satellite and Surface-based Quantitative Precipitation Estimation during the Colorado Flood

    NASA Astrophysics Data System (ADS)

    Kucera, Paul; Klepp, Christian; Newman, Andrew

    2015-04-01

    During the period of 9-16 September 2013, a large area of greater than 150 mm of rain, with local amounts of up to 450 mm, fell over a large part of the Colorado Front Range foothills and adjacent plains. This extreme rainfall event caused severe flooding of main river channels and some localized flash flooding which resulted in millions of dollars of damage to private and public properties. The rainfall regime associated with this extreme precipitation event was atypical of storms usually observed in this region. As a result, the satellite and radar rainfall algorithms tuned for this region significantly underestimated the total amount of rainfall. In order to quantify the underestimation and provide insight for improving the radar rainfall estimates for this unique precipitation regime, a comparison study has been conducted using data from several disdrometers that were operating throughout the event. Disdrometers observed over 5000 minutes of rainfall during the event. Analysis of the raindrop spectra indicated that most of the rainfall was comprised of a large number of small drops (< 2 mm in diameter). The raindrop spectra have been stratified by the precipitation regime. For these different regimes, new radar rainfall estimators have been derived from the raindrop spectra. The new estimators have been applied to the radar data to provide new rainfall estimates. These estimates along with satellite-based precipitation estimates have been evaluated using independent rain gauge data. The presentation will provide an overview of the Colorado flood and a summary of results from the precipitation estimation development and analysis.

  17. 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. PMID:27498986

  18. 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

  19. 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

  20. FPGA-based fused smart-sensor for tool-wear area quantitative estimation in CNC machine inserts.

    PubMed

    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

  1. 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

  2. Quantitative software models for the estimation of cost, size, and defects

    NASA Technical Reports Server (NTRS)

    Hihn, J.; Bright, L.; Decker, B.; Lum, K.; Mikulski, C.; Powell, J.

    2002-01-01

    The presentation will provide a brief overview of the SQI measurement program as well as describe each of these models and how they are currently being used in supporting JPL project, task and software managers to estimate and plan future software systems and subsystems.

  3. Toward a Quantitative Estimate of Future Heat Wave Mortality under Global Climate Change

    PubMed Central

    Peng, Roger D.; Bobb, Jennifer F.; Tebaldi, Claudia; McDaniel, Larry; Bell, Michelle L.; Dominici, Francesca

    2011-01-01

    Background Climate change is anticipated to affect human health by changing the distribution of known risk factors. Heat waves have had debilitating effects on human mortality, and global climate models predict an increase in the frequency and severity of heat waves. The extent to which climate change will harm human health through changes in the distribution of heat waves and the sources of uncertainty in estimating these effects have not been studied extensively. Objectives We estimated the future excess mortality attributable to heat waves under global climate change for a major U.S. city. Methods We used a database comprising daily data from 1987 through 2005 on mortality from all nonaccidental causes, ambient levels of particulate matter and ozone, temperature, and dew point temperature for the city of Chicago, Illinois. We estimated the associations between heat waves and mortality in Chicago using Poisson regression models. Results Under three different climate change scenarios for 2081–2100 and in the absence of adaptation, the city of Chicago could experience between 166 and 2,217 excess deaths per year attributable to heat waves, based on estimates from seven global climate models. We noted considerable variability in the projections of annual heat wave mortality; the largest source of variation was the choice of climate model. Conclusions The impact of future heat waves on human health will likely be profound, and significant gains can be expected by lowering future carbon dioxide emissions. PMID:21193384

  4. Estimation of Current Breed Differences in Multibreed Genetic Evaluations Using Quantitative and Molecular Approaches

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objectives of this presentation were to review methods used in multibreed approaches in national cattle evaluation, suggest guidelines for utilizing information for research estimates of breed differences, describe the design of the multibreed research program (germplasm evaluation; GPE) at the ...

  5. 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.

  6. 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. PMID:19430173

  7. Quantitative structure-activity relationships for the toxicity of nitrobenzenes to Tetrahymena thermophila.

    PubMed

    Xu, Jing-Bo; Jing, Ti-Song; Pauli, W; Berger, S

    2002-01-01

    In this study IGC50 (50% inhibitory growth concentration) values of 26 nitrobenzenes were determined for population growth endpoint of Tetrahymena thermophila. The toxicity order of the observed compounds has been found as follows: dinitro compounds > mono-nitro compounds; dichloronitrobenzenes > monochloronitrobenzenes; and meta-substituted nitrobenzenes > ortho-/para-substituted nitrobenzenes (NT, NPh, NAnis) except for the dinitrobenzenes and nitroanilines (DNB, NAn). Quantitative structure activity relationships (QSARs) were developed using log of the inverse of the IGC50 (logIGC50(-1)) in mole liter as the dependent variable and six molecular descriptors--logP, 1X(V), I, K alpha, sigma sigma- and E(LUMO) as the independent variables. Through multiplicate regression analysis, one best equation was obtained: log IGC50(-1) = 2.93 + 0.830sigma sigma- + 0.350I, n = 26, r = 0.923, r2 = 0.852, s = 0.265, f = 66.4 The equation was used to estimate IGC50 for seven analogues. PMID:12046656

  8. Quantitative estimation of thermal contact conductance of a real front-end component at SPring-8 front-ends.

    PubMed

    Sano, Mutsumi; Takahashi, Sunao; Mochizuki, Tetsuro; Watanabe, Atsuo; Oura, Masaki; Kitamura, Hideo

    2008-01-01

    The thermal contact conductance (TCC) of a real front-end component at SPring-8 has been quantitatively estimated by comparing the results of experiments with those of finite-element analyses. In this paper one of the methods of predicting the TCC of a real instrument is presented. A metal filter assembly, which is an indirect-cooling instrument, was selected for the estimation of the TCC. The temperature of the metal filter assembly for the maximum heat load of synchrotron radiation was calculated from the TCC that is expected under normal conditions. This study contributes towards the ongoing research program being conducted to investigate the real thermal limitation of all front-end high-heat-load components. PMID:18097071

  9. 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.

  10. [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. PMID:22242490

  11. 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.

  12. 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.

  13. 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.

  14. A quantitative method to estimate high gloss polished tool steel surfaces

    NASA Astrophysics Data System (ADS)

    Rebeggiani, S.; Rosén, B.-G.; Sandberg, A.

    2011-08-01

    Visual estimations are today the most common way to assess the surface quality of moulds and dies; a method that are both subjective and, with today's high demands on surfaces, hardly usable to distinguish between the finest surface qualities. Instead a method based on non-contact 3D-surface texture analysis is suggested. Several types of tool steel samples, manually as well as machine polished, were analysed to study different types of surface defects such as pitting, orange peel and outwardly features. The classification of the defect structures serves as a catalogue where known defects are described. Suggestions of different levels of 'high surface quality' defined in numerical values adapted to high gloss polished tool steel surfaces are presented. The final goal is to develop a new manual that can work as a 'standard' for estimations of tool steel surfaces for steel producers, mould makers, polishers etc.

  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 television fluoroangiography - the optical measurement of dye concentrations and estimation of retinal blood flow

    SciTech Connect

    Greene, M.; Thomas, A.L. Jr.

    1985-06-01

    The development of a system for the measurement of dye concentrations from single retinal vessels during retinal fluorescein angiography is presented and discussed. The system uses a fundus camera modified for TV viewing. Video gating techniques define the areas of the retina to be studied, and video peak detection yields dye concentrations from retinal vessels. The time course of dye concentration is presented and blood flow into the retina is estimated by a time of transit technique.

  17. Microwave Quantitative NDE Technique for Dielectric Slab Thickness Estimation Using the Music Algorithm

    NASA Astrophysics Data System (ADS)

    Abou-Khousa, M. A.; Zoughi, R.

    2007-03-01

    Non-invasive monitoring of dielectric slab thickness is of great interest in various industrial applications. This paper focuses on estimating the thickness of dielectric slabs, and consequently monitoring their variations, utilizing wideband microwave signals and the MUtiple SIgnal Characterization (MUSIC) algorithm. The performance of the proposed approach is assessed by validating simulation results with laboratory experiments. The results clearly indicate the utility of this overall approach for accurate dielectric slab thickness evaluation.

  18. 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.

  19. Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes

    PubMed Central

    Cooper, Gregory M.; Brudno, Michael; Program, NISC Comparative Sequencing; Green, Eric D.; Batzoglou, Serafim; Sidow, Arend

    2003-01-01

    Comparative sequence analyses on a collection of carefully chosen mammalian genomes could facilitate identification of functional elements within the human genome and allow quantification of evolutionary constraint at the single nucleotide level. High-resolution quantification would be informative for determining the distribution of important positions within functional elements and for evaluating the relative importance of nucleotide sites that carry single nucleotide polymorphisms (SNPs). Because the level of resolution in comparative sequence analyses is a direct function of sequence diversity, we propose that the information content of a candidate mammalian genome be defined as the sequence divergence it would add relative to already-sequenced genomes. We show that reliable estimates of genomic sequence divergence can be obtained from small genomic regions. On the basis of a multiple sequence alignment of ∼1.4 megabases each from eight mammals, we generate such estimates for five unsequenced mammals. Estimates of the neutral divergence in these data suggest that a small number of diverse mammalian genomes in addition to human, mouse, and rat would allow single nucleotide resolution in comparative sequence analyses. [The multiple sequence alignment of the CFTR region and a spreadsheet with the calculations performed, will be available as supplementary information online at www.genome.org.] PMID:12727901

  20. 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

  1. 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

  2. The Use of Multi-Sensor Quantitative Precipitation Estimates for Deriving Extreme Precipitation Frequencies with Application in Louisiana

    NASA Astrophysics Data System (ADS)

    El-Dardiry, Hisham Abd El-Kareem

    The Radar-based Quantitative Precipitation Estimates (QPE) is one of the NEXRAD products that are available in a high temporal and spatial resolution compared with gauges. Radar-based QPEs have been widely used in many hydrological and meteorological applications; however, a few studies have focused on using radar QPE products in deriving of Precipitation Frequency Estimates (PFE). Accurate and regionally specific information on PFE is critically needed for various water resources engineering planning and design purposes. This study focused first on examining the data quality of two main radar products, the near real-time Stage IV QPE product, and the post real-time RFC/MPE product. Assessment of the Stage IV product showed some alarming data artifacts that contaminate the identification of rainfall maxima. Based on the inter-comparison analysis of the two products, Stage IV and RFC/MPE, the latter was selected for the frequency analysis carried out throughout the study. The precipitation frequency analysis approach used in this study is based on fitting Generalized Extreme Value (GEV) distribution as a statistical model for the hydrologic extreme rainfall data that based on Annual Maximum Series (AMS) extracted from 11 years (2002-2012) over a domain covering Louisiana. The parameters of the GEV model are estimated using method of linear moments (L-moments). Two different approaches are suggested for estimating the precipitation frequencies; Pixel-Based approach, in which PFEs are estimated at each individual pixel and Region-Based approach in which a synthetic sample is generated at each pixel by using observations from surrounding pixels. The region-based technique outperforms the pixel based estimation when compared with results obtained by NOAA Atlas 14; however, the availability of only short record of observations and the underestimation of radar QPE for some extremes causes considerable reduction in precipitation frequencies in pixel-based and region

  3. Active learning applied for photometric redshift estimation of quasars

    NASA Astrophysics Data System (ADS)

    Han, Bo; Zhang, Yanxia; Zhao, Yongheng

    2015-08-01

    For a long time the quasars’ photometric redshifts have been estimated by learning from all available training dataset. In the scenario of big data, the amount of available data is huge and the dataset may include noise. Consequently, a major research challenge is to design a learning process that gains the most informative data from the available dataset in terms of optimal learning of the underlying relationships. By filtering out noisy data and redundant data, the optimal learning can improve both estimation accuracy and speed. Towards this objective, in this study we figure out an active learning approach that automatically learns a series of suppport vector regression models based on small size of different sampling data chunks. These models are applied on a validation dataset. By active learning, those validation data with estimation results vary in a certain range are regarded as the informative data and are aggregated in multiple training datasets. Next, the aggregated training datasets are combined into an ensemble estimator through averaging and then applied on a test dataset. Our experimental results on SDSS data show that the proposed method is helpful to improve quasars’ photometric redshift estimation accuracy.

  4. 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. PMID:25818089

  5. 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

  6. Quantitative DNA metabarcoding: improved estimates of species proportional biomass using correction factors derived from control material.

    PubMed

    Thomas, Austen C; Deagle, Bruce E; Eveson, J Paige; Harsch, Corie H; Trites, Andrew W

    2016-05-01

    DNA metabarcoding is a powerful new tool allowing characterization of species assemblages using high-throughput amplicon sequencing. The utility of DNA metabarcoding for quantifying relative species abundances is currently limited by both biological and technical biases which influence sequence read counts. We tested the idea of sequencing 50/50 mixtures of target species and a control species in order to generate relative correction factors (RCFs) that account for multiple sources of bias and are applicable to field studies. RCFs will be most effective if they are not affected by input mass ratio or co-occurring species. In a model experiment involving three target fish species and a fixed control, we found RCFs did vary with input ratio but in a consistent fashion, and that 50/50 RCFs applied to DNA sequence counts from various mixtures of the target species still greatly improved relative abundance estimates (e.g. average per species error of 19 ± 8% for uncorrected vs. 3 ± 1% for corrected estimates). To demonstrate the use of correction factors in a field setting, we calculated 50/50 RCFs for 18 harbour seal (Phoca vitulina) prey species (RCFs ranging from 0.68 to 3.68). Applying these corrections to field-collected seal scats affected species percentages from individual samples (Δ 6.7 ± 6.6%) more than population-level species estimates (Δ 1.7 ± 1.2%). Our results indicate that the 50/50 RCF approach is an effective tool for evaluating and correcting biases in DNA metabarcoding studies. The decision to apply correction factors will be influenced by the feasibility of creating tissue mixtures for the target species, and the level of accuracy needed to meet research objectives. PMID:26602877

  7. 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.

  8. Bragg peak prediction from quantitative proton computed tomography using different path estimates.

    PubMed

    Wang, Dongxu; Mackie, T Rockwell; Tomé, Wolfgang A

    2011-02-01

    This paper characterizes the performance of the straight-line path (SLP) and cubic spline path (CSP) as path estimates used in reconstruction of proton computed tomography (pCT). The GEANT4 Monte Carlo simulation toolkit is employed to simulate the imaging phantom and proton projections. SLP, CSP and the most-probable path (MPP) are constructed based on the entrance and exit information of each proton. The physical deviations of SLP, CSP and MPP from the real path are calculated. Using a conditional proton path probability map, the relative probability of SLP, CSP and MPP are calculated and compared. The depth dose and Bragg peak are predicted on the pCT images reconstructed using SLP, CSP, and MPP and compared with the simulation result. The root-mean-square physical deviations and the cumulative distribution of the physical deviations show that the performance of CSP is comparable to MPP while SLP is slightly inferior. About 90% of the SLP pixels and 99% of the CSP pixels lie in the 99% relative probability envelope of the MPP. Even at an imaging dose of ∼0.1 mGy the proton Bragg peak for a given incoming energy can be predicted on the pCT image reconstructed using SLP, CSP, or MPP with 1 mm accuracy. This study shows that SLP and CSP, like MPP, are adequate path estimates for pCT reconstruction, and therefore can be chosen as the path estimation method for pCT reconstruction, which can aid the treatment planning and range prediction of proton radiation therapy. PMID:21212472

  9. 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

  10. 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. PMID:26112367

  11. 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.

  12. Theoretical framework for quantitatively estimating ultrasound beam intensities using infrared thermography.

    PubMed

    Myers, Matthew R; Giridhar, Dushyanth

    2011-06-01

    In the characterization of high-intensity focused ultrasound (HIFU) systems, it is desirable to know the intensity field within a tissue phantom. Infrared (IR) thermography is a potentially useful method for inferring this intensity field from the heating pattern within the phantom. However, IR measurements require an air layer between the phantom and the camera, making inferences about the thermal field in the absence of the air complicated. For example, convection currents can arise in the air layer and distort the measurements relative to the phantom-only situation. Quantitative predictions of intensity fields based upon IR temperature data are also complicated by axial and radial diffusion of heat. In this paper, mathematical expressions are derived for use with IR temperature data acquired at times long enough that noise is a relatively small fraction of the temperature trace, but small enough that convection currents have not yet developed. The relations were applied to simulated IR data sets derived from computed pressure and temperature fields. The simulation was performed in a finite-element geometry involving a HIFU transducer sonicating upward in a phantom toward an air interface, with an IR camera mounted atop an air layer, looking down at the heated interface. It was found that, when compared to the intensity field determined directly from acoustic propagation simulations, intensity profiles could be obtained from the simulated IR temperature data with an accuracy of better than 10%, at pre-focal, focal, and post-focal locations. PMID:21682428

  13. 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

  14. 4-Aminoquinolines Active against Chloroquine-Resistant Plasmodium falciparum: Basis of Antiparasite Activity and Quantitative Structure-Activity Relationship Analyses▿

    PubMed Central

    Hocart, Simon J.; Liu, Huayin; Deng, Haiyan; De, Dibyendu; Krogstad, Frances M.; Krogstad, Donald J.

    2011-01-01

    Chloroquine (CQ) is a safe and economical 4-aminoquinoline (AQ) antimalarial. However, its value has been severely compromised by the increasing prevalence of CQ resistance. This study examined 108 AQs, including 68 newly synthesized compounds. Of these 108 AQs, 32 (30%) were active only against CQ-susceptible Plasmodium falciparum strains and 59 (55%) were active against both CQ-susceptible and CQ-resistant P. falciparum strains (50% inhibitory concentrations [IC50s], ≤25 nM). All AQs active against both CQ-susceptible and CQ-resistant P. falciparum strains shared four structural features: (i) an AQ ring without alkyl substitution, (ii) a halogen at position 7 (Cl, Br, or I but not F), (iii) a protonatable nitrogen at position 1, and (iv) a second protonatable nitrogen at the end of the side chain distal from the point of attachment to the AQ ring via the nitrogen at position 4. For activity against CQ-resistant parasites, side chain lengths of ≤3 or ≥10 carbons were necessary but not sufficient; they were identified as essential factors by visual comparison of 2-dimensional (2-D) structures in relation to the antiparasite activities of the AQs and were confirmed by computer-based 3-D comparisons and differential contour plots of activity against P. falciparum. The advantage of the method reported here (refinement of quantitative structure-activity relationship [QSAR] descriptors by random assignment of compounds to multiple training and test sets) is that it retains QSAR descriptors according to their abilities to predict the activities of unknown test compounds rather than according to how well they fit the activities of the compounds in the training sets. PMID:21383099

  15. 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

  16. Object orientated automated image analysis: quantitative and qualitative estimation of inflammation in mouse lung

    PubMed Central

    Apfeldorfer, Coralie; Ulrich, Kristina; Jones, Gareth; Goodwin, David; Collins, Susie; Schenck, Emanuel; Richard, Virgile

    2008-01-01

    Historically, histopathology evaluation is performed by a pathologist generating a qualitative assessment on thin tissue sections on glass slides. In the past decade, there has been a growing interest for tools able to reduce human subjectivity and improve workload. Whole slide scanning technology combined with object orientated image analysis can offer the capacity of generating fast and reliable results. In the present study, we combined the use of these emerging technologies to characterise a mouse model for chronic asthma. We monitored the inflammatory changes over five weeks by measuring the number of neutrophils and eosinophils present in the tissue, as well as, the bronchiolar associated lymphoid tissue (BALT) area on whole lungs sections. We showed that inflammation assessment could be automated efficiently and reliably. In comparison to human evaluation performed on the same set of sections, computer generated data was more descriptive and fully quantitative. Moreover optimisation of our detection parameters allowed us to be to more sensitive and to generate data in a larger dynamic range to traditional experimental evaluation, such as bronchiolar lavage (BAL) inflammatory cell counts obtained by flow cytometry. We also took advantage of the fact that we could increase the number of samples to be analysed within a day. Such optimisation allowed us to determine the best study design and experimental conditions in order to increase statistical significance between groups. In conclusion, we showed that combination of whole slide digital scanning and image analysis could be fully automated and deliver more descriptive and biologically relevant data over traditional methods evaluating histopathological pulmonary changes observed in this mouse model of chronic asthma. PMID:18673504

  17. Quantitative estimation of aesthesiometric thresholds for assessing impaired tactile sensation in workers exposed to vibration.

    PubMed

    Bovenzi, M; Zadini, A

    1989-01-01

    To evaluate the usefulness of aesthesiometric threshold testing in the quantitative assessment of peripheral sensorineural disorders occurring in the hand-arm vibration syndrome, two point discrimination (TPD) and depth sense perception (DSP) thresholds were measured by means of two aesthesiometers in the fingertips of 65 forestry workers exposed to chain saw vibration and 91 healthy males unexposed to local vibration or neurotoxic chemicals. Among the healthy subjects, divided into three age groups, there was no difference in the mean values of TPD and DSP thresholds. Assuming 1.28 or 2 standard deviations above the mean to be the upper limits of normality, in the present study the threshold values for TPD were 2.5 and 3.13 mm, respectively. Using the same assumptions, the normal threshold values for DSP were 0.36 and 0.49 mm. Among the 65 chain saw operators the prevalence of peripheral sensory disturbances was 70.8%. On the basis of the aesthesiometric results obtained for the group of 46 chain sawyers affected with sensorineural symptoms and a control group of 46 manual workers, the specificity of the aesthesiometric testing method was found to range between 93.4 and 100%, while the sensitivity varied from 52.2 to 71.7%. In its predictive value aesthesiometry had a positive accuracy of 84.6-96.0% and a negative accuracy of 42.8-50.0%. Aesthesiometric testing was able to differentiate between normals and vibration workers with sensory disturbances on a group basis (P less than 0.001), but due to the high rate of false negatives among vibration exposed patients, it was unsuitable to confirm objectively sensorineural symptoms on an individual basis.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:2777386

  18. Evaluating the capabilities of Sentinel-2 for quantitative estimation of biophysical variables in vegetation

    NASA Astrophysics Data System (ADS)

    Frampton, William James; Dash, Jadunandan; Watmough, Gary; Milton, Edward James

    2013-08-01

    The red edge position (REP) in the vegetation spectral reflectance is a surrogate measure of vegetation chlorophyll content, and hence can be used to monitor the health and function of vegetation. The Multi-Spectral Instrument (MSI) aboard the future ESA Sentinel-2 (S-2) satellite will provide the opportunity for estimation of the REP at much higher spatial resolution (20 m) than has been previously possible with spaceborne sensors such as Medium Resolution Imaging Spectrometer (MERIS) aboard ENVISAT. This study aims to evaluate the potential of S-2 MSI sensor for estimation of canopy chlorophyll content, leaf area index (LAI) and leaf chlorophyll concentration (LCC) using data from multiple field campaigns. Included in the assessed field campaigns are results from SEN3Exp in Barrax, Spain composed of 35 elementary sampling units (ESUs) of LCC and LAI which have been assessed for correlation with simulated MSI data using a CASI airborne imaging spectrometer. Analysis also presents results from SicilyS2EVAL, a campaign consisting of 25 ESUs in Sicily, Italy supported by a simultaneous Specim Aisa-Eagle data acquisition. In addition, these results were compared to outputs from the PROSAIL model for similar values of biophysical variables in the ESUs. The paper in turn assessed the scope of S-2 for retrieval of biophysical variables using these combined datasets through investigating the performance of the relevant Vegetation Indices (VIs) as well as presenting the novel Inverted Red-Edge Chlorophyll Index (IRECI) and Sentinel-2 Red-Edge Position (S2REP). Results indicated significant relationships between both canopy chlorophyll content and LAI for simulated MSI data using IRECI or the Normalised Difference Vegetation Index (NDVI) while S2REP and the MERIS Terrestrial Chlorophyll Index (MTCI) were found to have the strongest correlation for retrieval of LCC.

  19. On-line, adaptive state estimator for active noise control

    NASA Technical Reports Server (NTRS)

    Lim, Tae W.

    1994-01-01

    Dynamic characteristics of airframe structures are expected to vary as aircraft flight conditions change. Accurate knowledge of the changing dynamic characteristics is crucial to enhancing the performance of the active noise control system using feedback control. This research investigates the development of an adaptive, on-line state estimator using a neural network concept to conduct active noise control. In this research, an algorithm has been developed that can be used to estimate displacement and velocity responses at any locations on the structure from a limited number of acceleration measurements and input force information. The algorithm employs band-pass filters to extract from the measurement signal the frequency contents corresponding to a desired mode. The filtered signal is then used to train a neural network which consists of a linear neuron with three weights. The structure of the neural network is designed as simple as possible to increase the sampling frequency as much as possible. The weights obtained through neural network training are then used to construct the transfer function of a mode in z-domain and to identify modal properties of each mode. By using the identified transfer function and interpolating the mode shape obtained at sensor locations, the displacement and velocity responses are estimated with reasonable accuracy at any locations on the structure. The accuracy of the response estimates depends on the number of modes incorporated in the estimates and the number of sensors employed to conduct mode shape interpolation. Computer simulation demonstrates that the algorithm is capable of adapting to the varying dynamic characteristics of structural properties. Experimental implementation of the algorithm on a DSP (digital signal processing) board for a plate structure is underway. The algorithm is expected to reach the sampling frequency range of about 10 kHz to 20 kHz which needs to be maintained for a typical active noise control

  20. 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.

  1. QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS FOR CHEMICAL REDUCTIONS OF ORGANIC CONTAMINANTS

    EPA Science Inventory

    Sufficient kinetic data on abiotic reduction reactions involving organic contaminants are now available that quantitative structure-activity relationships (QSARs) for these reactions can be developed. Over 50 QSARs have been reported, most in just the last few years, and they ar...

  2. 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

  3. 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.

  4. [Quantitative estimation of glycyrrhizic acid and liquiritin contents using in-situ canopy spectroscopy].

    PubMed

    Ding, Ling; Li, Hong-Yi; Zhang, Xue-Wen

    2014-07-01

    The present study is the first to attempt to apply the in situ hyperspectral data of G. uralensis canopy in visible-shortwave infrared region (Vis-SWIR) to estimate quantification of GA and LQ contents of glycyrrhiza uralensis. After first derivative preprocessing and feature bands selection by Wilks' lambda stepwise method, partial least squares (PLS) regression with high performance liquid chromatography (HPLC) as reference was constructed to predict the value of GA and LQ contents, respectively. With the nine selected bands and PLS regression model, GA regression accuracy of R2 is 0.953, root mean square errors of calibration set (RMSEC) is 0.31, prediction accuracy R2 is 0.875 and root mean square errors of validation set (RMSEP) is 0.39; LQ regression accuracy of R2 is 0.932, RMSEC is 0.22, prediction accuracy R2 is 0.883 and RMSEP is 0.27; The results showed that our methods provided acceptable results and implied the ability of determining GA and LQ contents from remotely sensed data. It is recommended that an advanced study be conducted in field condition using airborne and/or spaceborne hyperspectral sensors. PMID:25269311

  5. A generalized estimating equations approach to quantitative trait locus detection of non-normal traits

    PubMed Central

    Thomson, Peter C

    2003-01-01

    To date, most statistical developments in QTL detection methodology have been directed at continuous traits with an underlying normal distribution. This paper presents a method for QTL analysis of non-normal traits using a generalized linear mixed model approach. Development of this method has been motivated by a backcross experiment involving two inbred lines of mice that was conducted in order to locate a QTL for litter size. A Poisson regression form is used to model litter size, with allowances made for under- as well as over-dispersion, as suggested by the experimental data. In addition to fixed parity effects, random animal effects have also been included in the model. However, the method is not fully parametric as the model is specified only in terms of means, variances and covariances, and not as a full probability model. Consequently, a generalized estimating equations (GEE) approach is used to fit the model. For statistical inferences, permutation tests and bootstrap procedures are used. This method is illustrated with simulated as well as experimental mouse data. Overall, the method is found to be quite reliable, and with modification, can be used for QTL detection for a range of other non-normally distributed traits. PMID:12729549

  6. A generalized estimating equations approach to quantitative trait locus detection of non-normal traits.

    PubMed

    Thomson, Peter C

    2003-01-01

    To date, most statistical developments in QTL detection methodology have been directed at continuous traits with an underlying normal distribution. This paper presents a method for QTL analysis of non-normal traits using a generalized linear mixed model approach. Development of this method has been motivated by a backcross experiment involving two inbred lines of mice that was conducted in order to locate a QTL for litter size. A Poisson regression form is used to model litter size, with allowances made for under- as well as over-dispersion, as suggested by the experimental data. In addition to fixed parity effects, random animal effects have also been included in the model. However, the method is not fully parametric as the model is specified only in terms of means, variances and covariances, and not as a full probability model. Consequently, a generalized estimating equations (GEE) approach is used to fit the model. For statistical inferences, permutation tests and bootstrap procedures are used. This method is illustrated with simulated as well as experimental mouse data. Overall, the method is found to be quite reliable, and with modification, can be used for QTL detection for a range of other non-normally distributed traits. PMID:12729549

  7. A new quantitative approach for estimating bone cell connections from nano-CT images.

    PubMed

    Dong, Pei; Pacureanu, Alexandra; Zuluaga, Maria A; Olivier, Cécile; Frouin, Frédérique; Grimal, Quentin; Peyrin, Françoise

    2013-01-01

    Recent works highlighted the crucial role of the osteocyte system in bone fragility. The number of canaliculi of osteocyte lacuna (Lc.NCa) is an important parameter that reflects the functionality of bone tissue, but rarely reported due to the limitations of current microscopy techniques, and only assessed from 2D histology sections. Previously, we showed the Synchrotron Radiation nanotomography (SR-nanoCT) is a promising technique to image the 3D lacunar-canalicular network. Here we present, for the first time, an automatic method to quantify the connectivity of bone cells in 3D. After segmentation, our method first separates and labels each lacuna in the network. Then, by creating a bounding surface around lacuna, the Lc.NCa is calculated through estimating 3D topological parameters. The proposed method was successfully applied to a 3D SR-nanoCT image of cortical femoral bone. Statistical results on 165 lacunae are reported, showing a mean of 51, which is consistent with the literature. PMID:24110532

  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. Suppression of irrelevant activation in the horizontal and vertical Simon task differs quantitatively not qualitatively.

    PubMed

    Töbel, Lisa; Hübner, Ronald; Stürmer, Birgit

    2014-10-01

    The Simon effect is usually explained by the assumption that the irrelevant stimulus location automatically activates the corresponding response. In the case of incongruent stimulus-response assignments automatically activated responses therefore have to be suppressed to ensure correct responses. This account, however, has been called into question for other than horizontally arranged visual Simon tasks. We investigated whether there is a qualitative or quantitative difference in suppression of irrelevant activation between horizontally and vertically arranged Simon tasks, using delta-function analyses. Sequential analyses revealed suppression after incongruent trials in both tasks, supporting the idea of a quantitative rather than a qualitative difference between the tasks. We conclude that automatic response activation is weaker in vertical tasks resulting in lower inhibitory demands as compared to horizontal tasks. PMID:25113126

  10. Application of quantitative estimates of fecal hemoglobin concentration for risk prediction of colorectal neoplasia

    PubMed Central

    Liao, Chao-Sheng; Lin, Yu-Min; Chang, Hung-Chuen; Chen, Yu-Hung; Chong, Lee-Won; Chen, Chun-Hao; Lin, Yueh-Shih; Yang, Kuo-Ching; Shih, Chia-Hui

    2013-01-01

    AIM: To determine the role of the fecal immunochemical test (FIT), used to evaluate fecal hemoglobin concentration, in the prediction of histological grade and risk of colorectal tumors. METHODS: We enrolled 17881 individuals who attended the two-step colorectal cancer screening program in a single hospital between January 2010 and October 2011. Colonoscopy was recommended to the participants with an FIT of ≥ 12 ngHb/mL buffer. We classified colorectal lesions as cancer (C), advanced adenoma (AA), adenoma (A), and others (O) by their colonoscopic and histological findings. Multiple linear regression analysis adjusted for age and gender was used to determine the association between the FIT results and colorectal tumor grade. The risk of adenomatous neoplasia was estimated by calculating the positive predictive values for different FIT concentrations. RESULTS: The positive rate of the FIT was 10.9% (1948/17881). The attendance rate for colonoscopy was 63.1% (1229/1948). The number of false positive results was 23. Of these 1229 cases, the numbers of O, A, AA, and C were 759, 221, 201, and 48, respectively. Regression analysis revealed a positive association between histological grade and FIT concentration (β = 0.088, P < 0.01). A significant log-linear relationship was found between the concentration and positive predictive value of the FIT for predicting colorectal tumors (R2 > 0.95, P < 0.001). CONCLUSION: Higher FIT concentrations are associated with more advanced histological grades. Risk prediction for colorectal neoplasia based on individual FIT concentrations is significant and may help to improve the performance of screening programs. PMID:24363529

  11. 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.

  12. A Quantitative Method to Estimate Vulnerability. Case Study: Motozintla de Mendoza, Chiapas

    NASA Astrophysics Data System (ADS)

    Rodriguez, F.; Novelo-Casanova, D. A.

    2011-12-01

    The community of Motozintla de Mendoza is located in the State of Chiapas, México (15' 22' N and 92' 15' W) near to the international border with Guatemala. Due to its location, this community is continuously exposed to many different hazards. Motozintla has a population of 20,000 inhabitants. This community suffered the impact of had two disasters recently. In view of these scenarios we carried out the present research with the objective quantifying the vulnerability of this community. We prepared a tool that allow us to document the physical vulnerability conducting interviews with people in risk situation. Our tool included the analysis of five elements: household structure and public services, socioeconomic characteristics, community preparation for facing a disaster situation, and risk perception of the inhabitants using a sample statistically significant. Three field works were carried out (October and November 2009, and October 2010) and 444 interviews were registered. Five levels of vulnerability were considered: very high, high, middle, moderate and low. Our region of study was classified spatially and the different estimated levels of vulnerability were located in geo referenced on maps. Our results indicate that the locality has a high level of physical vulnerability because about 74% of the population reports that their household had suffered damages in the past; 86% of the households present low resistance building materials; 70% of the interviewed families has a daily income under five to fifteen dollars; 66% of population does not know any existing Civil Protection Plan; 83% of the population considers that they live in a high level of risk due to floods; finally, the community organization is practically nonexistent. In conclusion, the level of vulnerability of Motozintla is high due to the many factors to which is exposed, in addition, to the structural, socioeconomic and cultural characteristics of their inhabitants. Evidently, those elements of

  13. 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.

  14. 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. PMID:21549039

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. Quantitative Estimates of Cloudiness over the Gulf Stream Locale Using GOES VAS Observations.

    NASA Astrophysics Data System (ADS)

    Alliss, Randall J.; Raman, Sethu

    1995-02-01

    Fields of cloudiness derived from the Geostationary Operational Environmental Satellite VISSR (Visible Infrared Spin Scan Radiometer) Atmospheric Sounder are analyzed over the Gulf Stream locale (GSL) to investigate seasonal and geographical variations. The GSL in this study is defined as the region bounded from 31° to 38°N and 82° to 66°W. This region covers an area that includes the United States mid-Atlantic coast states, the Gulf Stream, and portions of the Sargasso Sea. Clouds over the GSL are found approximately three-quarters of the time between 1985 and 1993. However, large seasonal variations in the frequency of cloudiness exist. These seasonal variations show a distinct relationship to gradients in sea surface temperature (SST). For example, during winter when large SST gradients are present, large gradients in cloudiness are found. Clouds are observed least often during summer over the ocean portion of the GSL. This minimum coincides with an increase in atmospheric stability due to large-scale subsidence. Cloudiness is also found over the GSL in response to mesoscale convergence areas induced by sea surface temperature gradients. Geographical variations in cloudiness are found to be related to the meteorology of the region. During periods of cold-air advection, which are found most frequently in winter, clouds are found less often between the coastline and the core of the Gulf Stream and more often over the Sargasso Sea. During cyclogenesis, large cloud shields often develop and cover the entire domain.Satellite estimates of cloudiness are found to be least reliable over land at night during the cold months. In these situations, the cloud retrieval algorithm often mistakes clear sky for low clouds. Satellite-derived cloudiness over land is compared with daytime surface observations of cloudiness. Results indicate that retrieved cloudiness agrees well with surface observations. Relative humidity fields taken from global analyses are compared with

  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. [Quantitative Analysis of Immuno-fluorescence of Nuclear Factor-κB Activation].

    PubMed

    Xiu, Min; He, Feng; Lou, Yuanlei; Xu, Lu; Xiong Jieqi; Wang, Ping; Liu, Sisun; Guo, Fei

    2015-06-01

    Immuno-fluorescence technique can qualitatively determine certain nuclear translocation, of which NF-κB/ p65 implicates the activation of NF-κB signal pathways. Immuno-fluorescence analysis software with independent property rights is able to quantitatively analyze dynamic location of NF-κB/p65 by computing relative fluorescence units in nuclei and cytoplasm. We verified the quantitative analysis by Western Blot. When we applied the software to analysis of nuclear translocation in lipopolysaccharide (LPS) induced (0. 5 h, 1 h, 2 h, 4 h) primary human umbilical vein endothelial cells (HUVECs) , we found that nuclear translocation peak showed up at 2h as with calculated Western blot verification results, indicating that the inventive immuno-fluorescence analysis software can be applied to the quantitative analysis of immuno-fluorescence. PMID:26485997

  3. Estimation of restraint stress in rats using salivary amylase activity.

    PubMed

    Matsuura, Tetsuya; Takimura, Ryo; Yamaguchi, Masaki; Ichinose, Mitsuyuki

    2012-09-01

    The rat is an ideal model animal for studying physical and psychological stresses. Recent human studies have shown that salivary amylase activity is a useful biomarker of stress in our social life. To estimate the usefulness of amylase activity as a biomarker of stress in rats, we analyzed changes in physiological parameters including amylase activity and anatomical variables, which were induced by a mild restraint of paws (10 min, 3 times/week, 9 weeks). The quantities of food and water intake and excretion amount of the stress rats were smaller than those of the control rats during the experimental period (5-13 weeks). The body weight of the stress rats decreased compared with that of the control rats. Moreover, the enlargement of the adrenal gland was confirmed in the stress rats, indicating that the mild restraint caused a chronic stress response. The amylase activities of the stress rats were significantly greater than those of the control rats at 5 weeks of age. However, the amylase activity of the stress rats decreased compared with that of the control rats after 6 weeks of age. These results indicate that amylase activity is increased by acute stress and reduced by chronic stress, which is caused by repeated restraint stress. In conclusion, amylase activity is a useful biomarker of acute and chronic stresses in rats. PMID:22753135

  4. Quantitative structure-activity relationship models with receptor-dependent descriptors for predicting peroxisome proliferator-activated receptor activities of thiazolidinedione and oxazolidinedione derivatives.

    PubMed

    Lather, Viney; Kairys, Visvaldas; Fernandes, Miguel X

    2009-04-01

    A quantitative structure-activity relationship study has been carried out, in which the relationship between the peroxisome proliferator-activated receptor alpha and the peroxisome proliferator-activated receptor gamma agonistic activities of thiazolidinedione and oxazolidinedione derivatives and quantitative descriptors, V(site) calculated in a receptor-dependent manner is modeled. These descriptors quantify the volume occupied by the optimized ligands in regions that are either common or specific to the superimposed binding sites of the targets under consideration. The quantitative structure-activity relationship models were built by forward stepwise linear regression modeling for a training set of 27 compounds and validated for a test set of seven compounds, resulting in a squared correlation coefficient value of 0.90 for peroxisome proliferator-activated receptor alpha and of 0.89 for peroxisome proliferator-activated receptor gamma. The leave-one-out cross-validation and test set predictability squared correlation coefficient values for these models were 0.85 and 0.62 for peroxisome proliferator-activated receptor alpha and 0.89 and 0.50 for peroxisome proliferator-activated receptor gamma respectively. A dual peroxisome proliferator-activated receptor model has also been developed, and it indicates the structural features required for the design of ligands with dual peroxisome proliferator-activated receptor activity. These quantitative structure-activity relationship models show the importance of the descriptors here introduced in the prediction and interpretation of the compounds affinity and selectivity. PMID:19243388

  5. 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.

  6. Development of combination tapered fiber-optic biosensor dip probe for quantitative estimation of interleukin-6 in serum samples

    NASA Astrophysics Data System (ADS)

    Wang, Chun Wei; Manne, Upender; Reddy, Vishnu B.; Oelschlager, Denise K.; Katkoori, Venkat R.; Grizzle, William E.; Kapoor, Rakesh

    2010-11-01

    A combination tapered fiber-optic biosensor (CTFOB) dip probe for rapid and cost-effective quantification of proteins in serum samples has been developed. This device relies on diode laser excitation and a charged-coupled device spectrometer and functions on a technique of sandwich immunoassay. As a proof of principle, this technique was applied in a quantitative estimation of interleukin IL-6. The probes detected IL-6 at picomolar levels in serum samples obtained from a patient with lupus, an autoimmune disease, and a patient with lymphoma. The estimated concentration of IL-6 in the lupus sample was 5.9 +/- 0.6 pM, and in the lymphoma sample, it was below the detection limit. These concentrations were verified by a procedure involving bead-based xMAP technology. A similar trend in the concentrations was observed. The specificity of the CTFOB dip probes was assessed by analysis with receiver operating characteristics. This analysis suggests that the dip probes can detect 5-pM or higher concentration of IL-6 in these samples with specificities of 100%. The results provide information for guiding further studies in the utilization of these probes to quantify other analytes in body fluids with high specificity and sensitivity.

  7. 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.

  8. 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

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

    PubMed

    Zhang, Wenchao; Dai, Xinbin; Wang, Qishan; Xu, Shizhong; Zhao, Patrick X

    2016-05-01

    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

  10. Why keep the pressure to estimate prokaryotic activities? (Invited)

    NASA Astrophysics Data System (ADS)

    Tamburini, C.

    2013-12-01

    Recent discoveries challenge the paradigm that cycling of organic matter is slow in the deep sea and mediated by microbial food webs of static structure and function. Data showing spatial variation in prokaryotic abundance and activity support the hypothesis that deep-sea microorganisms respond dynamically to variations in organic matter input to the bathypelagic realm. Moreover, almost half of the total water column heterotrophic prokaryotic production takes place below the epipelagic layer. Compiled global budgets suggest that the estimate of metabolic activity in the dark pelagic ocean exceeds the input of organic carbon. However, these conclusions are based mainly on measurements done at atmospheric pressure without taking into account pressure effects on natural prokaryotic assemblages. In this presentation, I will clarify the effect of hydrostatic pressure on prokaryotes living in the dark ocean and inform experimental design and the achievement of more accurate estimates of microbial activity in the deep ocean. Finally, their potential capabilities to degrade complex compounds as well as the chemolithoautrophy in the deep ocean represent examples of ways to explore deeper the role of deep-sea prokaryotes in the global cycles.

  11. 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

  12. Methods for quantitative detection of antibody-induced complement activation on red blood cells.

    PubMed

    Meulenbroek, Elisabeth M; Wouters, Diana; Zeerleder, Sacha

    2014-01-01

    Antibodies against red blood cells (RBCs) can lead to complement activation resulting in an accelerated clearance via complement receptors in the liver (extravascular hemolysis) or leading to intravascular lysis of RBCs. Alloantibodies (e.g. ABO) or autoantibodies to RBC antigens (as seen in autoimmune hemolytic anemia, AIHA) leading to complement activation are potentially harmful and can be - especially when leading to intravascular lysis - fatal(1). Currently, complement activation due to (auto)-antibodies on RBCs is assessed in vitro by using the Coombs test reflecting complement deposition on RBC or by a nonquantitative hemolytic assay reflecting RBC lysis(1-4). However, to assess the efficacy of complement inhibitors, it is mandatory to have quantitative techniques. Here we describe two such techniques. First, an assay to detect C3 and C4 deposition on red blood cells that is induced by antibodies in patient serum is presented. For this, FACS analysis is used with fluorescently labeled anti-C3 or anti-C4 antibodies. Next, a quantitative hemolytic assay is described. In this assay, complement-mediated hemolysis induced by patient serum is measured making use of spectrophotometric detection of the released hemoglobin. Both of these assays are very reproducible and quantitative, facilitating studies of antibody-induced complement activation. PMID:24514151

  13. 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. PMID:27367287

  14. Quantitative analysis of the relationship between nucleotide sequence and functional activity.

    PubMed Central

    Stormo, G D; Schneider, T D; Gold, L

    1986-01-01

    Matrices can be used to evaluate sequences for functional activity. Multiple regression can solve for the matrix that gives the best fit between sequence evaluations and quantitative activities. This analysis shows that the best model for context effects on suppression by su2 involves primarily the two nucleotides 3' to the amber codon, and that their contributions are independent and additive. Context effects on 2AP mutagenesis also involve the two nucleotides 3' to the 2AP insertion, but their effects are not independent. In a construct for producing beta-galactosidase, the effects on translational yields of the tri-nucleotide 5' to the initiation codon are dependent on the entire triplet. Models based on these quantitative results are presented for each of the examples. PMID:3092188

  15. 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

  16. Quantitative manganese tract tracing: dose-dependent and activity-independent terminal labelling in the mouse visual system.

    PubMed

    Lowe, Andrew S; Thompson, Ian D; Sibson, Nicola R

    2008-10-01

    At concentrations sufficient for visualisation using MRI, manganese (Mn) is believed to behave as a calcium analogue. This study examines different concentrations of Mn for enhanced MR tract tracing. The premise of activity-dependent axonal transport was also examined by partial or complete blockade of retinal ganglion cell activity. Quantitative T(1) maps and semi-quantitative normalised signal intensities in the superior colliculi facilitated assessment of applied intraocular concentrations and activity dependence, respectively. Varying the concentration of applied Mn revealed a non-monotonic profile, with optimal, unfavourable and undesirable effects noted: 25 mM proved optimal, showing a maximal decrease in T(1), whereas 400 mM was associated with no terminal-field enhancement. The estimated vitreal concentration for optimal transport of Mn (2 mM) is substantially lower than that used in previous studies of the mouse. Both the partial blockade of inputs to 50% of retinal ganglion cells by a mGluR6 glutamate agonist and the complete blockade of all retinal ganglion cell activity with tetrodotoxin failed to decrease the relative enhancement in the superior colliculus. The failure to prevent axonal transport of Mn by blocking activity (and therefore theoretically the intracellular influx) appeared to be paradoxical. The optimal vitreal concentration of Mn has previously been shown to facilitate massive intracellular uptake of Mn, competitively blocking calcium, and 1 mM Mn blocks neurotransmission pre-synaptically. These results suggest that, at concentrations required for optimal Mn-enhanced MRI tract tracing in the visual system of the mouse, the uptake and transport of Mn may be dominated by passive mechanisms, which may also block neurotransmission. PMID:18613265

  17. Estimating true human and animal host source contribution in quantitative microbial source tracking using the Monte Carlo method.

    PubMed

    Wang, Dan; Silkie, Sarah S; Nelson, Kara L; Wuertz, Stefan

    2010-09-01

    Cultivation- and library-independent, quantitative PCR-based methods have become the method of choice in microbial source tracking. However, these qPCR assays are not 100% specific and sensitive for the target sequence in their respective hosts' genome. The factors that can lead to false positive and false negative information in qPCR results are well defined. It is highly desirable to have a way of removing such false information to estimate the true concentration of host-specific genetic markers and help guide the interpretation of environmental monitoring studies. Here we propose a statistical model based on the Law of Total Probability to predict the true concentration of these markers. The distributions of the probabilities of obtaining false information are estimated from representative fecal samples of known origin. Measurement error is derived from the sample precision error of replicated qPCR reactions. Then, the Monte Carlo method is applied to sample from these distributions of probabilities and measurement error. The set of equations given by the Law of Total Probability allows one to calculate the distribution of true concentrations, from which their expected value, confidence interval and other statistical characteristics can be easily evaluated. The output distributions of predicted true concentrations can then be used as input to watershed-wide total maximum daily load determinations, quantitative microbial risk assessment and other environmental models. This model was validated by both statistical simulations and real world samples. It was able to correct the intrinsic false information associated with qPCR assays and output the distribution of true concentrations of Bacteroidales for each animal host group. Model performance was strongly affected by the precision error. It could perform reliably and precisely when the standard deviation of the precision error was small (≤ 0.1). Further improvement on the precision of sample processing and q

  18. Quantitative telomerase enzyme activity determination using droplet digital PCR with single cell resolution

    PubMed Central

    Ludlow, Andrew T.; Robin, Jerome D.; Sayed, Mohammed; Litterst, Claudia M.; Shelton, Dawne N.; Shay, Jerry W.; Wright, Woodring E.

    2014-01-01

    The telomere repeat amplification protocol (TRAP) for the human reverse transcriptase, telomerase, is a PCR-based assay developed two decades ago and is still used for routine determination of telomerase activity. The TRAP assay can only reproducibly detect ∼2-fold differences and is only quantitative when compared to internal standards and reference cell lines. The method generally involves laborious radioactive gel electrophoresis and is not conducive to high-throughput analyzes. Recently droplet digital PCR (ddPCR) technologies have become available that allow for absolute quantification of input deoxyribonucleic acid molecules following PCR. We describe the reproducibility and provide several examples of a droplet digital TRAP (ddTRAP) assay for telomerase activity, including quantitation of telomerase activity in single cells, telomerase activity across several common telomerase positive cancer cells lines and in human primary peripheral blood mononuclear cells following mitogen stimulation. Adaptation of the TRAP assay to digital format allows accurate and reproducible quantification of the number of telomerase-extended products (i.e. telomerase activity; 57.8 ± 7.5) in a single HeLa cell. The tools developed in this study allow changes in telomerase enzyme activity to be monitored on a single cell basis and may have utility in designing novel therapeutic approaches that target telomerase. PMID:24861623

  19. Quantitative Estimation of the Metal-Induced Negative Oxide Charge Density in n-Type Silicon Wafers from Measurements of Frequency-Dependent AC Surface Photovoltage

    NASA Astrophysics Data System (ADS)

    Shimizu, Hirofumi; Shin, Ryuhei; Ikeda, Masanori

    2006-03-01

    A quantitative estimation of metal-induced oxide charge (Qmi) density is performed on the surface of n-type silicon (Si) wafers rinsed with trivalent aluminum (Al)- and iron (Fe)-contaminated RCA alkaline solution by analyzing the frequency-dependent AC surface photovoltage (SPV). Qmi arises from (AlOSi)- or (FeOSi)- networks in native oxide which are responsible for inducing negative oxide charge. On the basis of Munakata and Nishimatsu’s half-sided junction model [C. Munakata and S. Nishimatsu: Jpn. J. Appl. Phys. 25 (1986) 807], the network densities are estimated in depletion and/or weak inversion in which the cutoff frequencies of the frequency-dependent AC SPV curves are defined. It is found that the charge density Qmi increases with the time of exposure to air and it is calculated that about 4% of Al atoms in the native oxide are activated in the form of an (AlOSi)- network for 1 h of exposure. The (FeOSi)- network density is calculated as a function of Fe concentration. As a result, the frequency-dependent AC SPV measurements carried out here enable a successful evaluation of impurity level in a nondestructive and noncontact manner.

  20. High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq.

    PubMed

    Vanhille, Laurent; Griffon, Aurélien; Maqbool, Muhammad Ahmad; Zacarias-Cabeza, Joaquin; Dao, Lan T M; Fernandez, Nicolas; Ballester, Benoit; Andrau, Jean Christophe; Spicuglia, Salvatore

    2015-01-01

    Cell-type specific regulation of gene expression requires the activation of promoters by distal genomic elements defined as enhancers. The identification and the characterization of enhancers are challenging in mammals due to their genome complexity. Here we develop CapStarr-Seq, a novel high-throughput strategy to quantitatively assess enhancer activity in mammals. This approach couples capture of regions of interest to previously developed Starr-seq technique. Extensive assessment of CapStarr-seq demonstrates accurate quantification of enhancer activity. Furthermore, we find that enhancer strength is associated with binding complexity of tissue-specific transcription factors and super-enhancers, while additive enhancer activity isolates key genes involved in cell identity and function. The CapStarr-Seq thus provides a fast and cost-effective approach to assess the activity of potential enhancers for a given cell type and will be helpful in decrypting transcription regulation mechanisms. PMID:25872643

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

    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).

  2. Estimation of Low Quantity Genes: A Hierarchical Model for Analyzing Censored Quantitative Real-Time PCR Data

    PubMed Central

    Boyer, Tim C.; Hanson, Tim; Singer, Randall S.

    2013-01-01

    Analysis of gene quantities measured by quantitative real-time PCR (qPCR) can be complicated by observations that are below the limit of quantification (LOQ) of the assay. A hierarchical model estimated using MCMC methods was developed to analyze qPCR data of genes with observations that fall below the LOQ (censored observations). Simulated datasets with moderate to very high levels of censoring were used to assess the performance of the model; model results were compared to approaches that replace censored observations with a value on the log scale approximating zero or with values ranging from one to the LOQ of ten gene copies. The model was also compared to a Tobit regression model. Finally, all approaches for handling censored observations were evaluated with DNA extracted from samples that were spiked with known quantities of the antibiotic resistance gene tetL. For the simulated datasets, the model outperformed substitution of all values from 1–10 under all censoring scenarios in terms of bias, mean square error, and coverage of 95% confidence intervals for regression parameters. The model performed as well or better than substitution of a value approximating zero under two censoring scenarios (approximately 57% and 79% censored values). The model also performed as well or better than Tobit regression in two of three censoring scenarios (approximately 79% and 93% censored values). Under the levels of censoring present in the three scenarios of this study, substitution of any values greater than 0 produced the least accurate results. When applied to data produced from spiked samples, the model produced the lowest mean square error of the three approaches. This model provides a good alternative for analyzing large amounts of left-censored qPCR data when the goal is estimation of population parameters. The flexibility of this approach can accommodate complex study designs such as longitudinal studies. PMID:23741414

  3. Activation autoradiography: imaging and quantitative determination of endogenous and exogenous oxygen in the rat brain

    SciTech Connect

    Kawashima, K.; Iwata, R.; Kogure, K.; Ohtomo, H.; Orihara, H.; Ido, T.

    1987-06-01

    Endogenous and exogenous oxygen in the rat brain were quantitatively determined using an autoradiographic technique. The oxygen images of frozen and dried rat brain sections were obtained as /sup 18/F images by using the /sup 16/O (/sup 3/He,p)/sup 18/F reaction for endogenous /sup 16/O images and the /sup 18/O(p,n)/sup 18/F reaction for endogenous and exogenous /sup 18/O images. These autoradiograms demonstrated the different distribution of oxygen between gray and white matter. These images also allowed differentiation of the individual structures of hippocampal formation, owing to the differing water content of the various structures. Local oxygen contents were quantitatively determined from autoradiograms of brain sections and standard sections with known oxygen contents. The estimated values were 75.6 +/- 4.6 wt% in gray matter and 72.2 +/- 4.0 wt% in white matter. The systematic error in the present method was estimated to be 4.9%.

  4. Quantitative structure-activity relationship models of clinical pharmacokinetics: clearance and volume of distribution.

    PubMed

    Gombar, Vijay K; Hall, Stephen D

    2013-04-22

    Reliable prediction of two fundamental human pharmacokinetic (PK) parameters, systemic clearance (CL) and apparent volume of distribution (Vd), determine the size and frequency of drug dosing and are at the heart of drug discovery and development. Traditionally, estimated CL and Vd are derived from preclinical in vitro and in vivo absorption, distribution, metabolism, and excretion (ADME) measurements. In this paper, we report quantitative structure-activity relationship (QSAR) models for prediction of systemic CL and steady-state Vd (Vdss) from intravenous (iv) dosing in humans. These QSAR models avoid uncertainty associated with preclinical-to-clinical extrapolation and require two-dimensional structure drawing as the sole input. The clean, uniform training sets for these models were derived from the compilation published by Obach et al. (Drug Metab. Disp. 2008, 36, 1385-1405). Models for CL and Vdss were developed using both a support vector regression (SVR) method and a multiple linear regression (MLR) method. The SVR models employ a minimum of 2048-bit fingerprints developed in-house as structure quantifiers. The MLR models, on the other hand, are based on information-rich electro-topological states of two-atom fragments as descriptors and afford reverse QSAR (RQSAR) analysis to help model-guided, in silico modulation of structures for desired CL and Vdss. The capability of the models to predict iv CL and Vdss with acceptable accuracy was established by randomly splitting data into training and test sets. On average, for both CL and Vdss, 75% of test compounds were predicted within 2.5-fold of the value observed and 90% of test compounds were within 5.0-fold of the value observed. The performance of the final models developed from 525 compounds for CL and 569 compounds for Vdss was evaluated on an external set of 56 compounds. The predictions were either better or comparable to those predicted by other in silico models reported in the literature. To

  5. 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

  6. 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

  7. Quantitative estimation of density variation in high-speed flows through inversion of the measured wavefront distortion

    NASA Astrophysics Data System (ADS)

    Medhi, Biswajit; Hegde, Gopalkrishna Mahadeva; Reddy, Kalidevapura Polareddy Jagannath; Roy, Debasish; Vasu, Ram Mohan

    2014-12-01

    A simple method employing an optical probe is presented to measure 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 random dot pattern. Local slopes of the distorted wavefront are obtained from shifts of the dots in the pattern. Local shifts in the dots are accurately measured by cross-correlating local shifted shadows with the corresponding unshifted originals. The measured slopes are suitably unwrapped by using a discrete cosine transform 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 5.8 measured using this technique are compared with the numerically estimated values.

  8. 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

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

    PubMed

    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

  10. 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.

  11. 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.

  12. 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

  13. Physical Activity in Vietnam: Estimates and Measurement Issues

    PubMed Central

    Bui, Tan Van; Blizzard, Christopher Leigh; Luong, Khue Ngoc; Truong, Ngoc Le Van; Tran, Bao Quoc; Otahal, Petr; Srikanth, Velandai; Nelson, Mark Raymond; Au, Thuy Bich; Ha, Son Thai; Phung, Hai Ngoc; Tran, Mai Hoang; Callisaya, Michele; Gall, Seana

    2015-01-01

    Introduction Our aims were to provide the first national estimates of physical activity (PA) for Vietnam, and to investigate issues affecting their accuracy. Methods Measurements were made using the Global Physical Activity Questionnaire (GPAQ) on a nationally-representative sample of 14706 participants (46.5% males, response 64.1%) aged 25−64 years selected by multi-stage stratified cluster sampling. Results Approximately 20% of Vietnamese people had no measureable PA during a typical week, but 72.9% (men) and 69.1% (women) met WHO recommendations for PA by adults for their age. On average, 52.0 (men) and 28.0 (women) Metabolic Equivalent Task (MET)-hours/week (largely from work activities) were reported. Work and total PA were higher in rural areas and varied by season. Less than 2% of respondents provided incomplete information, but an additional one-in-six provided unrealistically high values of PA. Those responsible for reporting errors included persons from rural areas and all those with unstable work patterns. Box-Cox transformation (with an appropriate constant added) was the most successful method of reducing the influence of large values, but energy-scaled values were most strongly associated with pathophysiological outcomes. Conclusions Around seven-in-ten Vietnamese people aged 25–64 years met WHO recommendations for total PA, which was mainly from work activities and higher in rural areas. Nearly all respondents were able to report their activity using the GPAQ, but with some exaggerated values and seasonal variation in reporting. Data transformation provided plausible summary values, but energy-scaling fared best in association analyses. PMID:26485044

  14. 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.

  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. Towards cheminformatics-based estimation of drug therapeutic index: Predicting the protective index of anticonvulsants using a new quantitative structure-index relationship approach.

    PubMed

    Chen, Shangying; Zhang, Peng; Liu, Xin; Qin, Chu; Tao, Lin; Zhang, Cheng; Yang, Sheng Yong; Chen, Yu Zong; Chui, Wai Keung

    2016-06-01

    The overall efficacy and safety profile of a new drug is partially evaluated by the therapeutic index in clinical studies and by the protective index (PI) in preclinical studies. In-silico predictive methods may facilitate the assessment of these indicators. Although QSAR and QSTR models can be used for predicting PI, their predictive capability has not been evaluated. To test this capability, we developed QSAR and QSTR models for predicting the activity and toxicity of anticonvulsants at accuracy levels above the literature-reported threshold (LT) of good QSAR models as tested by both the internal 5-fold cross validation and external validation method. These models showed significantly compromised PI predictive capability due to the cumulative errors of the QSAR and QSTR models. Therefore, in this investigation a new quantitative structure-index relationship (QSIR) model was devised and it showed improved PI predictive capability that superseded the LT of good QSAR models. The QSAR, QSTR and QSIR models were developed using support vector regression (SVR) method with the parameters optimized by using the greedy search method. The molecular descriptors relevant to the prediction of anticonvulsant activities, toxicities and PIs were analyzed by a recursive feature elimination method. The selected molecular descriptors are primarily associated with the drug-like, pharmacological and toxicological features and those used in the published anticonvulsant QSAR and QSTR models. This study suggested that QSIR is useful for estimating the therapeutic index of drug candidates. PMID:27262528

  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. 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.

  19. 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

  20. 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

  1. 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

  2. A quantitative way to estimate clinical off-target effects for human membrane brain targets in CNS research and development

    PubMed Central

    Spiros, Athan; Geerts, Hugo

    2012-01-01

    Although many preclinical programs in central nervous system research and development intend to develop highly selective and potent molecules directed at the primary target, they often act upon other off-target receptors. The simple rule of taking the ratios of affinities for the candidate drug at the different receptors is flawed since the affinity of the endogenous ligand for that off-target receptor or drug exposure is not taken into account. We have developed a mathematical receptor competition model that takes into account the competition between active drug moiety and the endogenous neurotransmitter to better assess the off-target effects on postsynaptic receptor activation under the correct target exposure conditions. As an example, we investigate the possible functional effects of the weak off-target effects for dopamine-1 receptor (D1R) in a computer simulation of a dopaminergic cortical synapse that is calibrated using published fast-cyclic rodent voltammetry and human imaging data in subjects with different catechol-O-methyltransferase genotypes. We identify the conditions under which off-target effects at the D1R can lead to clinically detectable consequences on cognitive tests, such as the N-back working memory test. We also demonstrate that certain concentrations of dimebolin (Dimebon), a recently tested Alzheimer drug, can affect D1R activation resulting in clinically detectable cognitive decrease. This approach can be extended to other receptor systems and can improve the selection of clinical candidate compounds by potentially dialing-out harmful off-target effects or dialing-in beneficial off-target effects in a quantitative and controlled way.

  3. Quantitation of fibroblast activation protein (FAP)-specific protease activity in mouse, baboon and human fluids and organs.

    PubMed

    Keane, Fiona M; Yao, Tsun-Wen; Seelk, Stefanie; Gall, Margaret G; Chowdhury, Sumaiya; Poplawski, Sarah E; Lai, Jack H; Li, Youhua; Wu, Wengen; Farrell, Penny; Vieira de Ribeiro, Ana Julia; Osborne, Brenna; Yu, Denise M T; Seth, Devanshi; Rahman, Khairunnessa; Haber, Paul; Topaloglu, A Kemal; Wang, Chuanmin; Thomson, Sally; Hennessy, Annemarie; Prins, John; Twigg, Stephen M; McLennan, Susan V; McCaughan, Geoffrey W; Bachovchin, William W; Gorrell, Mark D

    2013-01-01

    The protease fibroblast activation protein (FAP) is a specific marker of activated mesenchymal cells in tumour stroma and fibrotic liver. A specific, reliable FAP enzyme assay has been lacking. FAP's unique and restricted cleavage of the post proline bond was exploited to generate a new specific substrate to quantify FAP enzyme activity. This sensitive assay detected no FAP activity in any tissue or fluid of FAP gene knockout mice, thus confirming assay specificity. Circulating FAP activity was ∼20- and 1.3-fold less in baboon than in mouse and human plasma, respectively. Serum and plasma contained comparable FAP activity. In mice, the highest levels of FAP activity were in uterus, pancreas, submaxillary gland and skin, whereas the lowest levels were in brain, prostate, leukocytes and testis. Baboon organs high in FAP activity included skin, epididymis, bladder, colon, adipose tissue, nerve and tongue. FAP activity was greatly elevated in tumours and associated lymph nodes and in fungal-infected skin of unhealthy baboons. FAP activity was 14- to 18-fold greater in cirrhotic than in non-diseased human liver, and circulating FAP activity was almost doubled in alcoholic cirrhosis. Parallel DPP4 measurements concorded with the literature, except for the novel finding of high DPP4 activity in bile. The new FAP enzyme assay is the first to be thoroughly characterised and shows that FAP activity is measurable in most organs and at high levels in some. This new assay is a robust tool for specific quantitation of FAP enzyme activity in both preclinical and clinical samples, particularly liver fibrosis. PMID:24371721

  4. Quantitation of fibroblast activation protein (FAP)-specific protease activity in mouse, baboon and human fluids and organs☆

    PubMed Central

    Keane, Fiona M.; Yao, Tsun-Wen; Seelk, Stefanie; Gall, Margaret G.; Chowdhury, Sumaiya; Poplawski, Sarah E.; Lai, Jack H.; Li, Youhua; Wu, Wengen; Farrell, Penny; Vieira de Ribeiro, Ana Julia; Osborne, Brenna; Yu, Denise M.T.; Seth, Devanshi; Rahman, Khairunnessa; Haber, Paul; Topaloglu, A. Kemal; Wang, Chuanmin; Thomson, Sally; Hennessy, Annemarie; Prins, John; Twigg, Stephen M.; McLennan, Susan V.; McCaughan, Geoffrey W.; Bachovchin, William W.; Gorrell, Mark D.

    2013-01-01

    The protease fibroblast activation protein (FAP) is a specific marker of activated mesenchymal cells in tumour stroma and fibrotic liver. A specific, reliable FAP enzyme assay has been lacking. FAP's unique and restricted cleavage of the post proline bond was exploited to generate a new specific substrate to quantify FAP enzyme activity. This sensitive assay detected no FAP activity in any tissue or fluid of FAP gene knockout mice, thus confirming assay specificity. Circulating FAP activity was ∼20- and 1.3-fold less in baboon than in mouse and human plasma, respectively. Serum and plasma contained comparable FAP activity. In mice, the highest levels of FAP activity were in uterus, pancreas, submaxillary gland and skin, whereas the lowest levels were in brain, prostate, leukocytes and testis. Baboon organs high in FAP activity included skin, epididymis, bladder, colon, adipose tissue, nerve and tongue. FAP activity was greatly elevated in tumours and associated lymph nodes and in fungal-infected skin of unhealthy baboons. FAP activity was 14- to 18-fold greater in cirrhotic than in non-diseased human liver, and circulating FAP activity was almost doubled in alcoholic cirrhosis. Parallel DPP4 measurements concorded with the literature, except for the novel finding of high DPP4 activity in bile. The new FAP enzyme assay is the first to be thoroughly characterised and shows that FAP activity is measurable in most organs and at high levels in some. This new assay is a robust tool for specific quantitation of FAP enzyme activity in both preclinical and clinical samples, particularly liver fibrosis. PMID:24371721

  5. Mapping and Quantitation of the Interaction between the Recombination Activating Gene Proteins RAG1 and RAG2.

    PubMed

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

    2015-05-01

    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

  6. 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

  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. Quantitative estimation of the replication kinetics of genotype 2 PRRSV strains with different levels of virulence in vitro.

    PubMed

    Dong, Jianguo; Wang, Gang; Liu, Yonggang; Shi, Wenda; Wu, Jianan; Wen, Huiqiang; Wang, Shujie; Tian, Zhijun; Cai, Xuehui

    2016-08-01

    Porcine reproductive and respiratory syndrome virus (PRRSV) has become an important pathogen for the swine industry, and has resulted in substantial economic losses. In 2006, highly pathogenic PRRSV (HP-PRRSV) belonging to genotype 2 was first identified in China. Here, the replication kinetics of genotype 2 PRRSV strains were estimated in vitro in MARC-145 cells and porcine alveolar macrophages (PAMs) using a TaqMan-based real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay. The lower limit of detection was 10 copies/μL, and the assay was linear between 10(1) and 10(8) copies/μL. The intra-assay coefficients of variation were 0.81-1.36%, and the inter-assay coefficients of variation were 1.77-2.56%. Compared to the low pathogenicity CH-1a-F45 strain, the viral loads of the highly pathogenic HuN4-F45 strain were 10(0.5)-10(1.05) and 10(0.84)-10(1.35) times greater in MARC-145 cells and PAMs, respectively from 12 to 96h after infection (P<0.01). This study is the first to demonstrate that the HuN4-F45 strain replicated at higher levels than CH-1a-F45 in MARC-145 cells and PAMs, suggesting that HuN4-F45 has more robust virus amplification efficiency than CH-1a-F45 in vitro. PMID:27091099

  9. Activation energies of colloidal particle aggregation: towards a quantitative characterization of specific ion effects.

    PubMed

    Tian, Rui; Yang, Gang; Li, Hang; Gao, Xiaodan; Liu, Xinmin; Zhu, Hualing; Tang, Ying

    2014-05-21

    A quantitative description of specific ion effects is an essential and focused topic in colloidal and biological science. In this work, the dynamic light scattering technique was employed to study the aggregation kinetics of colloidal particles in the various alkali ion solutions with a wide range of concentrations. It indicated that the activation energies could be used to quantitatively characterize specific ion effects, which was supported by the results of effective hydrodynamic diameters, aggregation rates and critical coagulation concentrations. At a given concentration of 25 mmol L(-1), the activation energies for Li(+) are 1.2, 5.7, 28, and 126 times as much for Na(+), K(+), Rb(+), and Cs(+), respectively. Most importantly, the activation energy differences between two alkali cation species increase sharply with decrease of electrolyte concentrations, implying the more pronounced specific ion effects at lower concentrations. The dominant role of electrolyte cations during the aggregation of negatively charged colloidal particles was confirmed by alternative anions. Among the various theories, only the polarization effect can give a rational interpretation of the above specific ion effects, and this is substantially supported by the presence of strong electric fields from montmorillonite surfaces and its association mainly with electrolyte cations and montmorillonite particles. The classical induction theory, although with inclusion of electric field, requires significant corrections because it predicts an opposite trend to the experimentally observed specific ion effects. PMID:24603654

  10. Detection and semi-quantitative measurement of lung cancer metabolic activity by whole body PET

    SciTech Connect

    Tse, K.K.M.; Buchpiguel, C.A.; Alavi, J.B.

    1994-05-01

    Conventional radiologic and nuclear medicine techniques have been shown to have a limited role in the staging and monitoring of disease activity in patients with lung cancer. Both qualitative and semi-quantitative position emission tomography (PET) using the F-18 FDG technique have been applied to determine the clinical utility of whole body PET-FDG imaging in lung cancer. Nineteen whole body FDG PET scans were performed in 18 patients; 17 with lung cancer (15 non-small cell and 2 small cell) and 1 with squamous cell carcinoma of the trachea.

  11. Quantitative Measurement of Protease-Activity with Correction of Probe Delivery and Tissue Absorption Effects

    PubMed Central

    Salthouse, Christopher D.; Reynolds, Fred; Tam, Jenny M.; Josephson, Lee; Mahmood, Umar

    2009-01-01

    Proteases play important roles in a variety of pathologies from heart disease to cancer. Quantitative measurement of protease activity is possible using a novel spectrally matched dual fluorophore probe and a small animal lifetime imager. The recorded fluorescence from an activatable fluorophore, one that changes its fluorescent amplitude after biological target interaction, is also influenced by other factors including imaging probe delivery and optical tissue absorption of excitation and emission light. Fluorescence from a second spectrally matched constant (non-activatable) fluorophore on each nanoparticle platform can be used to correct for both probe delivery and tissue absorption. The fluorescence from each fluorophore is separated using fluorescence lifetime methods. PMID:20161242

  12. 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.

  13. QUANTITATIVE ESTIMATES OF SOIL INGESTION IN NORMAL CHILDREN BETWEEN THE AGES OF 2 AND 7 YEARS: POPULATION-BASED ESTIMATES USING ALUMINUM, SILICON, AND TITANIUM AS SOIL TRACER ELEMENTS

    EPA Science Inventory

    This investigation was undertaken to provide quantitative estimates of soil ingestion in young children on a population basis, and to identify demographic and behavioral characteristics that influence the amount of soil ingested. 04 children between the ages of 2 and 7 yr were se...

  14. 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. PMID:23702385

  15. 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...

  16. FISH ACUTE TOXICITY SYNDROMES: APPLICATION TO THE DEVELOPMENT OF MECHANISM-SPECIFIC QSARS (QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIPS)

    EPA Science Inventory

    Predictive models based on quantitative structure activity relationships (QSARs), are used as rapid screening tools to identify potentially hazardous chemicals. Several QSARs are now available that predict the acute toxicity of narcotic-industrial chemicals. Predictions for compo...

  17. FISH ACUTE TOXICITY SYNDROMES AND THEIR USE IN THE QSAR (QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP) APPROACH TO HAZARD ASSESSMENT

    EPA Science Inventory

    Implementation of the Toxic Substances Control Act of 1977 creates the need to reliably establish testing priorities because laboratory resources are limited and the number of industrial chemicals requiring evaluation is overwhelming. The use of quantitative structure activity re...

  18. 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

  19. A framework for the quantitative assessment of climate change impacts on water-related activities at the basin scale

    NASA Astrophysics Data System (ADS)

    Anghileri, D.; Pianosi, F.; Soncini-Sessa, R.

    2011-06-01

    While quantitative assessment of the climate change impact on hydrology at the basin scale is quite addressed in the literature, extension of quantitative analysis to impact on the ecological, economic and social sphere is still limited, although well recognized as a key issue to support water resource planning and promote public participation. In this paper we propose a framework for assessing climate change impact on water-related activities at the basin scale. The specific features of our approach are that: (i) the impact quantification is based on a set of performance indicators defined together with the stakeholders, thus explicitly taking into account the water-users preferences; (ii) the management policies are obtained by optimal control techniques, linking stakeholder expectations and decision-making; (iii) the multi-objective nature of the management problem is fully preserved by simulating a set of Pareto-optimal management policies, which allows for evaluating not only variations in the indicator values but also tradeoffs among conflicting objectives. The framework is demonstrated by application to a real world case study, Lake Como basin (Italy). We show that the most conflicting water-related activities within the basin (i.e. hydropower production and agriculture) are likely to be negatively impacted by climate change. We discuss the robustness of the estimated impacts to the climate natural variability and the approximations in modeling the physical system and the socio-economic system, and perform an uncertainty analysis of several sources of uncertainty. We demonstrate that the contribution of natural climate uncertainty is rather remarkable and that, among different modelling uncertainty sources, the one from climate modeling is very significant.

  20. A framework for the quantitative assessment of climate change impacts on water-related activities at the basin scale

    NASA Astrophysics Data System (ADS)

    Anghileri, D.; Pianosi, F.; Soncini-Sessa, R.

    2011-01-01

    While quantitative assessment of the climate change impact on hydrology at the basin scale is quite addressed in the literature, extension of quantitative analysis to impact on the ecological, economic and social sphere is still limited, although well recognized as a key issue to support water resource planning and promote public participation. In this paper we propose a framework for assessing climate change impact on water-related activities at the basin scale. The peculiarities of our approach are that: (i) the impact quantification is based on a set of performance indicators defined together with the stakeholders, thus explicitly taking into account the water-users preferences; (ii) the management policies are obtained by optimal control techniques, linking stakeholder expectations and decision-making; (iii) the multi-objective nature of the management problem is fully preserved by simulating a set of Pareto-optimal management policies, which allows for evaluating not only variations in the indicator values but also tradeoffs among conflicting objectives. The framework is demonstrated by application to a real world case study, Lake Como basin (Italy). We show that the most conflicting water-related activities within the basin (i.e. hydropower production and agriculture) are likely to be negatively impacted by climate change. An uncertainty analysis is performed in order to assess how the climate natural variability and approximations in modeling the physical system (climate and hydrology) and the socio-economic system (management policy) affect the robustness of the estimated impacts. We demonstrate that the contribution of natural climate uncertainty is rather significant and that, among different modelling uncertainty sources, the one from climate modeling is very significant.

  1. Dual enzyme activities assay by quantitative electrospray ionization quadrupole-time-of-flight mass spectrometry.

    PubMed

    Cai, Tingting; Zhang, Li; Wang, Haoyang; Zhang, Jing; Wang, Rong; Zhang, Yurong; Guo, Yinlong

    2012-01-01

    A practical and rapid method based on electrospray ionization quadrupole-time of flight mass spectrometry (ESI-Q-ToF MS) was developed for detecting activities of both acetylcholinesterase IAChEI and glutathione S-transferase (GST). The simultaneous study of these two enzyme activities is significant for studying human bio-functions, especially for those who take in toxic compounds and have a risk of disease. Here, the enzyme activities were represented by the conversion of enzymatic substrates and determined by quantitatively analyzing enzymatic substrates. Different internal standards were used to quantify each enzymatic substrate and the good linearity of calibration curves demonstrated the feasibility of the internal standards. The Michaelis-Menten constants (Km) of both GST and AChE were measured by this method and were consistent with values previously reported. Furthermore, we applied this approach to detect GST and AChE activities of whole bloods from four deceased and healthy people. The variation in enzyme activity was in accord with information from gas chromatography mass spectrometry [GC/MS). The screening of AChE and GST provided reliable results and strong forensic evidence. This method offers an alternative choice for detecting enzyme activities and is anticipated to have wide applications in pharmaceutical research and prevention in toxic compounds. PMID:23654197

  2. 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

  3. 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.

  4. Development and Validation of Quantitative Structure-Activity Relationship Models for Compounds Acting on Serotoninergic Receptors

    PubMed Central

    Żydek, Grażyna; Brzezińska, Elżbieta

    2012-01-01

    A quantitative structure-activity relationship (QSAR) study has been made on 20 compounds with serotonin (5-HT) receptor affinity. Thin-layer chromatographic (TLC) data and physicochemical parameters were applied in this study. RP2 TLC 60F254 plates (silanized) impregnated with solutions of propionic acid, ethylbenzene, 4-ethylphenol, and propionamide (used as analogues of the key receptor amino acids) and their mixtures (denoted as S1–S7 biochromatographic models) were used in two developing phases as a model of drug-5-HT receptor interaction. The semiempirical method AM1 (HyperChem v. 7.0 program) and ACD/Labs v. 8.0 program were employed to calculate a set of physicochemical parameters for the investigated compounds. Correlation and multiple linear regression analysis were used to search for the best QSAR equations. The correlations obtained for the compounds studied represent their interactions with the proposed biochromatographic models. The good multivariate relationships (R2 = 0.78–0.84) obtained by means of regression analysis can be used for predicting the quantitative effect of biological activity of different compounds with 5-HT receptor affinity. “Leave-one-out” (LOO) and “leave-N-out” (LNO) cross-validation methods were used to judge the predictive power of final regression equations. PMID:22619602

  5. 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.

  6. 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. PMID:17077558

  7. 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

  8. 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. PMID:26269461

  9. 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

  10. 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

  11. 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.

  12. Modelling Activities In Kinematics Understanding quantitative relations with the contribution of qualitative reasoning

    NASA Astrophysics Data System (ADS)

    Orfanos, Stelios

    2010-01-01

    In Greek traditional teaching a lot of significant concepts are introduced with a sequence that does not provide the students with all the necessary information required to comprehend. We consider that understanding concepts and the relations among them is greatly facilitated by the use of modelling tools, taking into account that the modelling process forces students to change their vague, imprecise ideas into explicit causal relationships. It is not uncommon to find students who are able to solve problems by using complicated relations without getting a qualitative and in-depth grip on them. Researchers have already shown that students often have a formal mathematical and physical knowledge without a qualitative understanding of basic concepts and relations." The aim of this communication is to present some of the results of our investigation into modelling activities related to kinematical concepts. For this purpose, we have used ModellingSpace, an environment that was especially designed to allow students from eleven to seventeen years old to express their ideas and gradually develop them. The ModellingSpace enables students to build their own models and offers the choice of observing directly simulations of real objects and/or all the other alternative forms of representations (tables of values, graphic representations and bar-charts). The students -in order to answer the questions- formulate hypotheses, they create models, they compare their hypotheses with the representations of their models and they modify or create other models when their hypotheses did not agree with the representations. In traditional ways of teaching, students are educated to utilize formulas as the most important strategy. Several times the students recall formulas in order to utilize them, without getting an in-depth understanding on them. Students commonly use the quantitative type of reasoning, since it is primarily used in teaching, although it may not be fully understood by them

  13. 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

  14. 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

  15. Structural and functional neural adaptations in obstructive sleep apnea: An activation likelihood estimation meta-analysis.

    PubMed

    Tahmasian, Masoud; Rosenzweig, Ivana; Eickhoff, Simon B; Sepehry, Amir A; Laird, Angela R; Fox, Peter T; Morrell, Mary J; Khazaie, Habibolah; Eickhoff, Claudia R

    2016-06-01

    Obstructive sleep apnea (OSA) is a common multisystem chronic disorder. Functional and structural neuroimaging has been widely applied in patients with OSA, but these studies have often yielded diverse results. The present quantitative meta-analysis aims to identify consistent patterns of abnormal activation and grey matter loss in OSA across studies. We used PubMed to retrieve task/resting-state functional magnetic resonance imaging and voxel-based morphometry studies. Stereotactic data were extracted from fifteen studies, and subsequently tested for convergence using activation likelihood estimation. We found convergent evidence for structural atrophy and functional disturbances in the right basolateral amygdala/hippocampus and the right central insula. Functional characterization of these regions using the BrainMap database suggested associated dysfunction of emotional, sensory, and limbic processes. Assessment of task-based co-activation patterns furthermore indicated that the two regions obtained from the meta-analysis are part of a joint network comprising the anterior insula, posterior-medial frontal cortex and thalamus. Taken together, our findings highlight the role of right amygdala, hippocampus and insula in the abnormal emotional and sensory processing in OSA. PMID:27039344

  16. 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.

  17. 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

  18. A simplified method for quantitative assessment of the relative health and safety risk of environmental management activities

    SciTech Connect

    Eide, S.A.; Smith, T.H.; Peatross, R.G.; Stepan, I.E.

    1996-09-01

    This report presents a simplified method to assess the health and safety risk of Environmental Management activities of the US Department of Energy (DOE). The method applies to all types of Environmental Management activities including waste management, environmental restoration, and decontamination and decommissioning. The method is particularly useful for planning or tradeoff studies involving multiple conceptual options because it combines rapid evaluation with a quantitative approach. The method is also potentially applicable to risk assessments of activities other than DOE Environmental Management activities if rapid quantitative results are desired.

  19. 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

  20. 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...

  1. Quantitative determination of residual active pharmaceutical ingredients and intermediates on equipment surfaces by ion mobility spectrometry.

    PubMed

    Qin, C; Granger, A; Papov, V; McCaffrey, J; Norwood, D L

    2010-01-01

    Ion mobility spectrometry (IMS) is an analytical technique that separates ions based on their gas phase mobility at atmospheric pressure. Since gas phase ion mobility is a function of the shape and structure of the ion, this technique has the potential to provide unique specificity and selectivity. Furthermore, IMS is very sensitive (subnanogram detection limits for many small molecules), and a single analysis is typically completed within 1 min. In principle, these features of IMS should make it an ideal choice for use in cleaning verification analysis of pharmaceutical manufacturing equipment. This report describes the successful development and validation of three different equipment cleaning verification methods using IMS. The methods were developed for a specific intermediate (Compound A) in the synthetic route for a drug substance as well as for final drug substances (active pharmaceutical ingredients Compounds B and C). The cleaning verification methods were validated with respect to specificity, linearity, precision, accuracy, stability, and limit-of-quantitation. In all cases, the limits-of-quantitation were determined to be at the nanogram or sub-nanogram level. Both swab and rinse samples collected from the equipment surfaces were successfully analyzed and manufacturing equipment down-time was significantly minimized due to the reduction in cleaning verification analysis time (for example, the total analysis time for more than 30 samples using IMS was reduced to less than 2h). PMID:19758781

  2. Dissecting eukaryotic cells by coherent phase microscopy: quantitative analysis of quiescent and activated T lymphocytes

    NASA Astrophysics Data System (ADS)

    Tychinsky, Vladimir P.; Kretushev, Alexander V.; Vyshenskaya, Tatiana V.; Shtil, Alexander A.

    2012-07-01

    We present a concept for quantitative characterization of a functional state of an individual eukaryotic cell based on interference imaging. The informative parameters of the phase images of quiescent and mitogen-activated T lymphocytes included the phase thickness, phase volume, the area, and the size of organelles. These parameters were obtained without a special hypothesis about cell structure. Combinations of these parameters generated a ``phase portrait'' of the cell. A simplified spherical multilayer optic model of a T lymphocyte was used to calculate the refractivity profile, to identify structural elements of the image with the organelles, and to interpret the parameters of the phase portrait. The values of phase image parameters underwent characteristic changes in the course of mitogenic stimulation of T cells; thereby, the functional state of individual cells can be described using these parameters. Because the values of the components of the phase portrait are measured in absolute units, it is possible to compare the parameters of images obtained with different interference microscopes. Thus, the analysis of phase portraits provides a new and perspective approach for quantitative, real-time analysis of subcellular structure and physiologic state of an individual cell.

  3. 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

  4. Quantitative study of impacts of climate change and human activities on runoff in Beiluohe River basin

    NASA Astrophysics Data System (ADS)

    Guo, A.; Huang, Q.; Wang, Y.

    2015-05-01

    In the Beiluohe River basin (BRB) runoff has been experiencing a significant reduction induced by climate change and human activities. This paper considers the impacts of climate change and human activities on runoff reduction. An improved empirical method for climate factors and runoff was developed to study the impacts quantitatively. Meanwhile climate elasticity of runoff, based on the Budyko hypothesis, was also adopted to study the impacts. Using runoff change points, series were divided into natural period (1960-1969) and impacted periods (1970-1994, 1995-2010). Results show that the methods used to quantify the contributions obtained different but close conclusions to one another. For 1970-1994, climate was the primary factor impacting runoff, compared with that for 1960-1969, with the contribution reaching around 70.84-83.42%, which was greater than human activities (16.58-29.16%). For 1995-2010, the role of human activities strengthened with the contribution around 62.58-65.07%, greater than climate changes, around 34.93-37.42%.

  5. Technology efficacy in active prosthetic knees for transfemoral amputees: a quantitative evaluation.

    PubMed

    El-Sayed, Amr M; Hamzaid, Nur Azah; 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

  6. 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

  7. Quantitative structure-activity analyses of novel hydroxyphenylurea derivatives as antioxidants.

    PubMed

    Nakao, K; Shimizu, R; Kubota, H; Yasuhara, M; Hashimura, Y; Suzuki, T; Fujita, T; Ohmizu, H

    1998-06-01

    A series of substituted hydroxyphenylureas was synthesized, the chemical structure of which was designed based on structures of natural antioxidants, vitamin E (alpha-tocopherol) and uric acid. They exhibited high inhibitory activity against lipid peroxidation. In order to gain an insight into the mechanism of the inhibition reaction, we analyzed their structure-activity relationships quantitatively. Electronic and steric effects of substituents on the phenolic hydroxyl group were shown to be of importance in governing the inhibitory potency. An increase in the electron donating property of substituents toward the phenolic hydroxyl group enhanced the antioxidative activity by the stabilization of an electron-deficient radical-type transition state. The steric shielding by ortho-substituents stabilized the phenoxy radicals formed following the transition state. Derivatives having the carboxyl group were only weakly active presumably because of an intermolecular ion-dipole interaction of the phenolic hydroxyl group with the carboxylate anion which could retard the formation of the transition state. PMID:9681151

  8. Comparison of quantitative k-edge empirical estimators using an energy-resolved photon-counting detector

    NASA Astrophysics Data System (ADS)

    Zimmerman, Kevin C.; Gilat Schmidt, Taly

    2016-03-01

    Using an energy-resolving photon counting detector, the amount of k-edge material in the x-ray path can be estimated using a process known as material decomposition. However, non-ideal effects within the detector make it difficult to accurately perform this decomposition. This work evaluated the k-edge material decomposition accuracy of two empirical estimators. A neural network estimator and a linearized maximum likelihood estimator with error look-up tables (A-table method) were evaluated through simulations and experiments. Each estimator was trained on system-specific calibration data rather than specific modeling of non-ideal detector effects or the x-ray source spectrum. Projections through a step-wedge calibration phantom consisting of different path lengths through PMMA, aluminum, and a k-edge material was used to train the estimators. The estimators were tested by decomposing data acquired through different path lengths of the basis materials. The estimators had similar performance in the chest phantom simulations with gadolinium. They estimated four of the five densities of gadolinium with less than 2mg/mL bias. The neural networks estimates demonstrated lower bias but higher variance than the A-table estimates in the iodine contrast agent simulations. The neural networks had an experimental variance lower than the CRLB indicating it is a biased estimator. In the experimental study, the k-edge material contribution was estimated with less than 14% bias for the neural network estimator and less than 41% bias for the A-table method.

  9. 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.

  10. 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.

  11. Active illumination using a digital micromirror device for quantitative phase imaging.

    PubMed

    Shin, Seungwoo; Kim, Kyoohyun; Yoon, Jonghee; Park, YongKeun

    2015-11-15

    We present a powerful and cost-effective method for active illumination using a digital micromirror device (DMD) for quantitative phase-imaging techniques. Displaying binary illumination patterns on a DMD with appropriate spatial filtering, plane waves with various illumination angles are generated and impinged onto a sample. Complex optical fields of the sample obtained with various incident angles are then measured via Mach-Zehnder interferometry, from which a high-resolution 2D synthetic aperture phase image and a 3D refractive index tomogram of the sample are reconstructed. We demonstrate the fast and stable illumination-control capability of the proposed method by imaging colloidal spheres and biological cells. The capability of high-speed optical diffraction tomography is also demonstrated by measuring 3D Brownian motion of colloidal particles with the tomogram acquisition rate of 100 Hz. PMID:26565886

  12. 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. PMID:27426856

  13. Quantitative conformationally sampled pharmacophore for delta opioid ligands: reevaluation of hydrophobic moieties essential for biological activity.

    PubMed

    Bernard, Denzil; Coop, Andrew; MacKerell, Alexander D

    2007-04-19

    Recent studies have indicated several therapeutic applications for delta opioid agonists and antagonists. To exploit the therapeutic potential of delta opioids developing a structural basis for the activity of ligands at the delta opioid receptor is essential. The conformationally sampled pharmacophore (CSP) method (Bernard et al. J. Am. Chem. Soc. 2003, 125, 3103-3107) is extended here to obtain quantitative models of delta opioid ligand efficacy and affinity. Quantification is performed via overlap integrals of the conformational space sampled by ligands with respect to a reference compound. Iterative refinement of the CSP model identified hydrophobic groups other than the traditional phenylalanine residues as important for efficacy and affinity in DSLET and ICI 174 864. The obtained models for a structurally diverse set of peptidic and nonpeptidic delta opioid ligands offer good predictions with R2 values>0.9, and the predicted efficacy for a set of test compounds was consistent with the experimental values. PMID:17367120

  14. Development of quantitative structure activity relationships for the binding affinity of methoxypyridinium cations for human acetylcholinesterase.

    PubMed

    Morrill, Jason A; Topczewski, Joseph J; Lodge, Alexander M; Yasapala, Nilanthi; Quinn, Daniel M

    2015-11-01

    Among the most toxic substances known are the organophosphorus (OP) compounds used as pesticides and chemical warfare agents. Owing to their high toxicity there is a number of efforts underway to develop effective therapies for OP agent exposure. To date all therapies in use treat inhibited acetylcholinesterase (AChE), but are ineffective for the treatment of inhibited AChE, which has undergone a subsequent hydrolysis process, referred to as aging. Toward developing a therapy for treating victims of OP intoxication in the aged state we have developed Quantitative Structure-Activity Relationships (QSARs) based on the AM1 semiempirical quantum mechanical method using the program, CODESSA (COmprehensive Descriptors for Structural and Statistical Analysis). Using this methodology we obtained a multiple correlation QSAR equation which gave R(2)=0.9359 for a random training set of 38 ligands and R(2)=0.9236 for prediction on a random test set of 9 ligands. PMID:26454505

  15. Quantitative structure-activity relationships for cellular uptake of surface-modified nanoparticles.

    PubMed

    Liu, Rong; Rallo, Robert; Bilal, Muhammad; Cohen, Yoram

    2015-01-01

    Quantitative structure-activity relationships (QSARs) were developed, for cellular uptake of nanoparticles (NPs) of the same iron oxide core but with different surface-modifying organic molecules, based on linear and non-linear (epsilon support vector regression (ε-SVR)). A linear QSAR provided high prediction accuracy of R2=0.751 (coefficient of determination) using 11 descriptors selected from an initial pool of 184 descriptors calculated for the NP surfacemodifying molecules, while a ε-SVR based QSAR with only 6 descriptors improved prediction accuracy to R2=0.806. The linear and ε-SVR based QSARs both demonstrated good robustness and well spanned applicability domains. It is suggested that the approach of evaluating pertinent descriptors and their significance, via QSAR analysis, to cellular NP uptake could support planning and interpretation of toxicity studies as well as provide guidance for the tailor-design NPs with respect to targeted cellular uptake for various applications. PMID:25747434

  16. Evaluation of a method for activity estimation in Sm-153 EDTMP imaging

    SciTech Connect

    Vanzi, Eleonora; Genovesi, Dario; Di Martino, Fabio

    2009-04-15

    Absolute activity evaluation is fundamental for internal radionuclide dosimetry when patient-specific therapy optimization is wanted. Often, quantification is attempted with 3D SPECT image based (IB) methods, but the true concentration values can be underestimated due to the partial volume effect (PVE). This is especially true when small diffuse lesions are present. In this paper, we describe a 3D region of interest (ROI) based quantification method (LS-ROI), which estimates the ROI concentration values directly from the projection data acquired in the tomographic scan once ROIs have been segmented on a CT and/or a SPECT image. The method, which has inherent PVE correction capabilities, was applied both on simulated and on real phantom data. Simulations reflected the case of a patient with bone metastases treated with {sup 153}Sm-EDTMP: Both the activity in the metastases and the total retention in the skeleton were evaluated. Thirty noisy data sets were produced in order to evaluate the accuracy and precision of the method. The effect of region segmentation errors on estimated concentrations was thoroughly investigated. Real data were acquired on a NEMA phantom, where a cylindrical central region (283 cm{sup 3}) simulated the bone and two spheres (10.3 and 25.5 cm{sup 3}) simulated the metastases. The results obtained with the LS-ROI method were compared with those of a conventional 3D IB method and those of a quantitative conjugate view approach derived from LS-ROI and applied to the anterior and posterior views acquired in the tomographic scan (LS-ROI anterior-posterior: LS-ROI-AP). Simulations showed that when the geometry of regions is known, the LS-ROI method recovered the simulated concentration values within 20%, while the IB method underestimated the concentration in high activity small lesions by as much as 49%. Segmentation errors, up to 44% of the true region volume, produced a higher variation in LS-ROI estimates than in IB ones; however, the overall

  17. HomoSAR: bridging comparative protein modeling with quantitative structural activity relationship to design new peptides.

    PubMed

    Borkar, Mahesh R; Pissurlenkar, Raghuvir R S; Coutinho, Evans C

    2013-11-15

    Peptides play significant roles in the biological world. To optimize activity for a specific therapeutic target, peptide library synthesis is inevitable; which is a time consuming and expensive. Computational approaches provide a promising way to simply elucidate the structural basis in the design of new peptides. Earlier, we proposed a novel methodology termed HomoSAR to gain insight into the structure activity relationships underlying peptides. Based on an integrated approach, HomoSAR uses the principles of homology modeling in conjunction with the quantitative structural activity relationship formalism to predict and design new peptide sequences with the optimum activity. In the present study, we establish that the HomoSAR methodology can be universally applied to all classes of peptides irrespective of sequence length by studying HomoSAR on three peptide datasets viz., angiotensin-converting enzyme inhibitory peptides, CAMEL-s antibiotic peptides, and hAmphiphysin-1 SH3 domain binding peptides, using a set of descriptors related to the hydrophobic, steric, and electronic properties of the 20 natural amino acids. Models generated for all three datasets have statistically significant correlation coefficients (r(2)) and predictive r2 (r(pred)2) and cross validated coefficient ( q(LOO)2). The daintiness of this technique lies in its simplicity and ability to extract all the information contained in the peptides to elucidate the underlying structure activity relationships. The difficulties of correlating both sequence diversity and variation in length of the peptides with their biological activity can be addressed. The study has been able to identify the preferred or detrimental nature of amino acids at specific positions in the peptide sequences. PMID:24105965

  18. 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

  19. 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

  20. 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.

  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. 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. PMID:24506443

  3. 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

  4. 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.

  5. 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. PMID:26832327

  6. 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

  7. 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. PMID:26513561

  8. 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.

  9. An advanced application of the quantitative structure-activity relationship concept in electrokinetic chromatography of metal complexes.

    PubMed

    Oszwałdowski, Sławomir; Timerbaev, Andrei R

    2008-02-01

    The relevance of the quantitative structure-activity relationship (QSAR) principle in MEKC and microemulsion EKC (MEEKC) of metal-ligand complexes was evaluated for a better understanding of analyte migration mechanism. A series of gallium chelates were applied as test solutes with available experimental migration data in order to reveal the molecular properties that govern the separation. The QSAR models operating with n-octanol-water partition coefficients or van der Waals volumes were found to be valid for estimation of the retention factors (log k') of neutral compounds when using only an aqueous MEEKC electrolyte. On the other hand, consistent approximations of log k' for both uncharged and charged complexes in either EKC mode (and also with hydro-organic BGEs) were achievable with two-parametric QSARs in which the dipole moment is additionally incorporated as a structural descriptor, reflecting the electrostatic solute-pseudostationary phase interaction. The theoretical analysis of significant molecular parameters in MEKC systems, in which the micellar BGE is modified with an organic solvent, confirmed that concomitant consideration of hydrophobic, electrostatic, and solvation factors is essential for explaining the migration behavior of neutral metal complexes. PMID:18219650

  10. Structural alerts for predicting clastogenic activity of pro-oxidant flavonoid compounds: quantitative structure-activity relationship study.

    PubMed

    Yordi, Estela Guardado; Pérez, Enrique Molina; Matos, Maria Joao; Villares, Eugenio Uriarte

    2012-02-01

    Flavonoids have been reported to exert multiple biological effects that include acting as pro-oxidants at very high doses. The authors determined a structural alert to identify the clastogenic activity of a series of flavonoids with pro-oxidant activity. The methodology was based on a quantitative structure-activity relationship (QSAR) study. Specifically, the authors developed a virtual screening method for a clastogenic model using the topological substructural molecular design (TOPS-MODE) approach. It represents a useful platform for the automatic generation of structural alerts, based on the calculation of spectral moments of molecular bond matrices appropriately weighted, taking into account the hydrophobic, electronic, and steric molecular features. Therefore, it was possible to establish the structural criteria for maximal clastogenicity of pro-oxidant flavonoids: the presence of a 3-hydroxyl group and a 4-carbonyl group in ring C, the maximal number of hydroxyl groups in ring B, the presence of methoxyl and phenyl groups, the absence of a 2,3-double bond in ring C, and the presence of 5,7 hydroxyl groups in ring A. The presented clastogenic model may be useful for screening new pro-oxidant compounds. This alert could help in the design of new and efficient flavonoids, which could be used as bioactive compounds in nutraceuticals and functional food. PMID:21940715

  11. 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

  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 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

  14. Quantitative Profiling of the Activity of Protein Lysine Methyltransferase SMYD2 Using SILAC-Based Proteomics.

    PubMed

    Olsen, Jonathan B; Cao, Xing-Jun; Han, Bomie; Chen, Lisa Hong; Horvath, Alexander; Richardson, Timothy I; Campbell, Robert M; Garcia, Benjamin A; Nguyen, Hannah

    2016-03-01

    The significance of non-histone lysine methylation in cell biology and human disease is an emerging area of research exploration. The development of small molecule inhibitors that selectively and potently target enzymes that catalyze the addition of methyl-groups to lysine residues, such as the protein lysine mono-methyltransferase SMYD2, is an active area of drug discovery. Critical to the accurate assessment of biological function is the ability to identify target enzyme substrates and to define enzyme substrate specificity within the context of the cell. Here, using stable isotopic labeling with amino acids in cell culture (SILAC) coupled with immunoaffinity enrichment of mono-methyl-lysine (Kme1) peptides and mass spectrometry, we report a comprehensive, large-scale proteomic study of lysine mono-methylation, comprising a total of 1032 Kme1 sites in esophageal squamous cell carcinoma (ESCC) cells and 1861 Kme1 sites in ESCC cells overexpressing SMYD2. Among these Kme1 sites is a subset of 35 found to be potently down-regulated by both shRNA-mediated knockdown of SMYD2 and LLY-507, a selective small molecule inhibitor of SMYD2. In addition, we report specific protein sequence motifs enriched in Kme1 sites that are directly regulated by endogenous SMYD2 activity, revealing that SMYD2 substrate specificity is more diverse than expected. We further show direct activity of SMYD2 toward BTF3-K2, PDAP1-K126 as well as numerous sites within the repetitive units of two unique and exceptionally large proteins, AHNAK and AHNAK2. Collectively, our findings provide quantitative insights into the cellular activity and substrate recognition of SMYD2 as well as the global landscape and regulation of protein mono-methylation. PMID:26750096

  15. Calcaneal Quantitative Ultrasound Indicates Reduced Bone Status Among Physically Active Adult Forager-Horticulturalists.

    PubMed

    Stieglitz, Jonathan; Madimenos, Felicia; Kaplan, Hillard; Gurven, Michael

    2016-03-01

    Sedentary lifestyle contributes to osteoporosis and fragility fracture risks among modern humans, but whether such risks are prevalent in physically active preindustrial societies with lower life expectancies is unclear. Osteoporosis should be readily observable in preindustrial societies if it was regularly experienced over human history. In this study of 142 older adult Tsimane forager-horticulturalists (mean age ± SD, 62.1 ± 8.6 years; range, 50 to 85 years; 51% female) we used calcaneal quantitative ultrasonography (qUS) to assess bone status, document prevalence of adults with reduced bone status, and identify factors (demographic, anthropometric, immunological, kinesthetic) associated with reduced bone status. Men (23%) are as likely as women (25%) to have reduced bone status, although age-related decline in qUS parameters is attenuated for men. Adiposity and fat-free mass positively co-vary with qUS parameters for women but not men. Leukocyte count is inversely associated with qUS parameters controlling for potential confounders; leukocyte count is positively correlated within adults over time, and adults with persistently low counts have higher adjusted qUS parameters (6% to 8%) than adults with a high count. Reduced bone status characteristic of osteoporosis is common among active Tsimane with minimal exposure to osteoporosis risk factors found in industrialized societies, but with energetic constraints and high pathogen burden. © 2015 American Society for Bone and Mineral Research. PMID:26460548

  16. Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

    PubMed Central

    Sigala, Paul A.; Fafarman, Aaron T.; Schwans, Jason P.; Fried, Stephen D.; Fenn, Timothy D.; Caaveiro, Jose M. M.; Pybus, Brandon; Ringe, Dagmar; Petsko, Gregory A.; Boxer, Steven G.; Herschlag, Daniel

    2013-01-01

    Hydrogen bond networks are key elements of protein structure and function but have been challenging to study within the complex protein environment. We have carried out in-depth interrogations of the proton transfer equilibrium within a hydrogen bond network formed to bound phenols in the active site of ketosteroid isomerase. We systematically varied the proton affinity of the phenol using differing electron-withdrawing substituents and incorporated site-specific NMR and IR probes to quantitatively map the proton and charge rearrangements within the network that accompany incremental increases in phenol proton affinity. The observed ionization changes were accurately described by a simple equilibrium proton transfer model that strongly suggests the intrinsic proton affinity of one of the Tyr residues in the network, Tyr16, does not remain constant but rather systematically increases due to weakening of the phenol–Tyr16 anion hydrogen bond with increasing phenol proton affinity. Using vibrational Stark spectroscopy, we quantified the electrostatic field changes within the surrounding active site that accompany these rearrangements within the network. We were able to model these changes accurately using continuum electrostatic calculations, suggesting a high degree of conformational restriction within the protein matrix. Our study affords direct insight into the physical and energetic properties of a hydrogen bond network within a protein interior and provides an example of a highly controlled system with minimal conformational rearrangements in which the observed physical changes can be accurately modeled by theoretical calculations. PMID:23798390

  17. 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. PMID:26153539

  18. 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. PMID:16041138

  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 proteomics analyses of activation states of human THP-1 macrophages.

    PubMed

    Meijer, Kees; Weening, Desiree; de Vries, Marcel P; Priebe, Marion G; Vonk, Roel J; Roelofsen, Han

    2015-10-14

    Macrophages display large functional and phenotypical plasticity. They can adopt a broad range of activation states depending on their microenvironment. Various surface markers are used to characterize these differentially polarized macrophages. However, this is not informative for the functions of the macrophage. In order to have a better understanding of the functional changes of macrophages upon differential polarization, we studied differences in LPS- and IL4-stimulated macrophages. The THP-1 human monocytic cell line, was used as a model system. Cells were labeled, differentiated and stimulated with either LPS or IL-4 in a quantitative SILAC proteomics set-up. The resulting sets of proteins were functionally clustered. LPS-stimulated macrophages show increased secretion of proinflammatory peptides, leading to increased pressure on protein biosynthesis and processing. IL4-stimulated macrophages show upregulation of cell adhesion and extracellular matrix remodeling. Our approach provides an integrated view of polarization-induced functional changes and proves useful for studying functional differences between subsets of macrophages. Moreover, the identified polarization specific proteins may contribute to a better characterization of different activation states in situ and their role in various inflammatory processes. PMID:26200757

  1. 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. PMID:24855045

  2. A new fusion protein platform for quantitatively measuring activity of multiple proteases

    PubMed Central

    2014-01-01

    Background Recombinant proteins fused with specific cleavage sequences are widely used as substrate for quantitatively analyzing the activity of proteases. Here we propose a new fusion platform for multiple proteases, by using diaminopropionate ammonia-lyase (DAL) as the fusion protein. It was based on the finding that a fused His6-tag could significantly decreases the activities of DAL from E. coli (eDAL) and Salmonella typhimurium (sDAL). Previously, we have shown that His6GST-tagged eDAL could be used to determine the activity of tobacco etch virus protease (TEVp) under different temperatures or in the denaturant at different concentrations. In this report, we will assay different tags and cleavage sequences on DAL for expressing yield in E. coli, stability of the fused proteins and performance of substrate of other common proteases. Results We tested seven different protease cleavage sequences (rhinovirus 3C, TEV protease, factor Xa, Ssp DnaB intein, Sce VMA1 intein, thrombin and enterokinase), three different tags (His6, GST, CBD and MBP) and two different DALs (eDAL and sDAL), for their performance as substrate to the seven corresponding proteases. Among them, we found four active DAL-fusion substrates suitable for TEVp, factor Xa, thrombin and DnaB intein. Enterokinase cleaved eDAL at undesired positions and did not process sDAL. Substitution of GST with MBP increase the expression level of the fused eDAL and this fusion protein was suitable as a substrate for analyzing activity of rhinovirus 3C. We demonstrated that SUMO protease Ulp1 with a N-terminal His6-tag or MBP tag displayed different activity using the designed His6SUMO-eDAL as substrate. Finally, owing to the high level of the DAL-fusion protein in E. coli, these protein substrates can also be detected directly from the crude extract. Conclusion The results show that our designed DAL-fusion proteins can be used to quantify the activities of both sequence- and conformational-specific proteases, with

  3. 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

  4. 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.

  5. 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

  6. Fully Automated Quantitative Estimation of Volumetric Breast Density from Digital Breast Tomosynthesis Images: Preliminary Results and Comparison with Digital Mammography and MR Imaging.

    PubMed

    Pertuz, Said; McDonald, Elizabeth S; Weinstein, Susan P; Conant, Emily F; Kontos, Despina

    2016-04-01

    Purpose To assess a fully automated method for volumetric breast density (VBD) estimation in digital breast tomosynthesis (DBT) and to compare the findings with those of full-field digital mammography (FFDM) and magnetic resonance (MR) imaging. Materials and Methods Bilateral DBT images, FFDM images, and sagittal breast MR images were retrospectively collected from 68 women who underwent breast cancer screening from October 2011 to September 2012 with institutional review board-approved, HIPAA-compliant protocols. A fully automated computer algorithm was developed for quantitative estimation of VBD from DBT images. FFDM images were processed with U.S. Food and Drug Administration-cleared software, and the MR images were processed with a previously validated automated algorithm to obtain corresponding VBD estimates. Pearson correlation and analysis of variance with Tukey-Kramer post hoc correction were used to compare the multimodality VBD estimates. Results Estimates of VBD from DBT were significantly correlated with FFDM-based and MR imaging-based estimates with r = 0.83 (95% confidence interval [CI]: 0.74, 0.90) and r = 0.88 (95% CI: 0.82, 0.93), respectively (P < .001). The corresponding correlation between FFDM and MR imaging was r = 0.84 (95% CI: 0.76, 0.90). However, statistically significant differences after post hoc correction (α = 0.05) were found among VBD estimates from FFDM (mean ± standard deviation, 11.1% ± 7.0) relative to MR imaging (16.6% ± 11.2) and DBT (19.8% ± 16.2). Differences between VDB estimates from DBT and MR imaging were not significant (P = .26). Conclusion Fully automated VBD estimates from DBT, FFDM, and MR imaging are strongly correlated but show statistically significant differences. Therefore, absolute differences in VBD between FFDM, DBT, and MR imaging should be considered in breast cancer risk assessment. (©) RSNA, 2015 Online supplemental material is available for this article. PMID:26491909

  7. 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

  8. 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

  9. Quantitative Phosphokinome Analysis of the Met Pathway Activated by the Invasin Internalin B from Listeria monocytogenes*

    PubMed Central

    Reinl, Tobias; Nimtz, Manfred; Hundertmark, Claudia; Johl, Thorsten; Kéri, György; Wehland, Jürgen; Daub, Henrik; Jänsch, Lothar

    2009-01-01

    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 iTRAQTM 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

  10. Quantitative meta-analysis of neural activity in posttraumatic stress disorder

    PubMed Central

    2012-01-01

    Background In recent years, neuroimaging techniques such as functional magnetic resonance imaging (fMRI) and positron emission tomography (PET) have played a significant role in elucidating the neural underpinnings of posttraumatic stress disorder (PTSD). However, a detailed understanding of the neural regions implicated in the disorder remains incomplete because of considerable variability in findings across studies. The aim of this meta-analysis was to identify consistent patterns of neural activity across neuroimaging study designs in PTSD to improve understanding of the neurocircuitry of PTSD. Methods We conducted a literature search for PET and fMRI studies of PTSD that were published before February 2011. The article search resulted in 79 functional neuroimaging PTSD studies. Data from 26 PTSD peer-reviewed neuroimaging articles reporting results from 342 adult patients and 342 adult controls were included. Peak activation coordinates from selected articles were used to generate activation likelihood estimate maps separately for symptom provocation and cognitive-emotional studies of PTSD. A separate meta-analysis examined the coupling between ventromedial prefrontal cortex and amygdala activity in patients. Results Results demonstrated that the regions most consistently hyperactivated in PTSD patients included mid- and dorsal anterior cingulate cortex, and when ROI studies were included, bilateral amygdala. By contrast, widespread hypoactivity was observed in PTSD including the ventromedial prefrontal cortex and the inferior frontal gyrus. Furthermore, decreased ventromedial prefrontal cortex activity was associated with increased amygdala activity. Conclusions These results provide evidence for a neurocircuitry model of PTSD that emphasizes alteration in neural networks important for salience detection and emotion regulation. PMID:22738125

  11. Geophysical Monitoring of Active Infiltration Experiments for Recharge Estimation: Gains and Pains

    NASA Astrophysics Data System (ADS)

    Noell, U.; Lamparter, A.; Houben, G.; Koeniger, P.; Stoeckl, L.; Guenther, T.

    2014-12-01

    Drinking water supply on the island of Langeoog, North Sea, solely depends on groundwater from a freshwater lens. The correct estimation of the recharge rate is critical for a sustainable use of the resource. Extensive hydrogeological and geophysical studies have revealed differences in groundwater recharge by a factor of two and more between the top of the dunes and the dune valleys. The most convincing proof of these differences in recharge is based on isotope analysis (age dating) but boreholes are scarce and a direct proof of recharge is desired. For this purpose active infiltration experiments are performed and geophysically monitored. Former applications of this method in sand and loess soil gave evidence for the applicability of the geophysical observation when combined with tensiometers installed in situ at depth. These results showed firstly that in sandy soil the water reaches the groundwater table quicker than anticipated due to the water repellent characteristic of the dry sand, inhibiting the lateral spreading of the water. The studies also revealed that in loess preferential flow is initiated by ponding and that sprinkling caused very slow movement of water within the unsaturated zone and the water remained near the surface. On the island of Langeoog field experiments underlined the importance of water repellency on the dune surface, indicating that the rain water runs off superficially into the dune valleys where higher recharge is found. The active infiltration zone of the experiment covers an area of some 7m² and includes steeper parts of the dune. The infiltration will vary depending on rainfall intensity and duration, original water content and vegetation cover. What results can we reliably expect from the active experiment and what additional measurements are required to back up the findings? Results are ambiguous with regard to the quantitative assessment but the processes can be visualized by geophysical monitoring in situ.

  12. 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. PMID:26522329

  13. 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. PMID:22834741

  14. A Correlative Study of Splenic Parasite Score and Peripheral Blood Parasite Load Estimation by Quantitative PCR in Visceral Leishmaniasis.

    PubMed

    Sudarshan, Medhavi; Singh, Toolika; Chakravarty, Jaya; Sundar, Shyam

    2015-12-01

    Parasitological diagnosis of visceral leishmaniasis (VL) by splenic smear is highly sensitive, but it is associated with the risk of severe hemorrhage. In this study, the diagnosis of VL using quantitative PCR (qPCR) in peripheral blood was evaluated in 100 patients with VL. Blood parasitemia ranged from 5 to 93,688 leishmania parasite genomes/ml of blood and positively correlated with splenic score (P<0.0001; r2=0.58). Therefore, quantification of parasite genomes by qPCR can replace invasive procedures for diagnostic and prognostic evaluations. PMID:26400788

  15. Quantitative structure-activity relationship models for prediction of the toxicity of polybrominated diphenyl ether congeners.

    PubMed

    Wang, Yawei; Liu, Huanxiang; Zhao, Chunyan; Liu, Hanxia; Cai, Zongwei; Jiang, Guibin

    2005-07-01

    Levels of polybrominated diphenyl ethers (PBDEs) are increasing in the environment and may cause long-term health problems in humans. The similarity in the chemical structures of PBDEs and other halogenated aromatic pollutants hints on the possibility that they might share similar toxicological effects. In this work, three-dimensional quantitative structure activity relationships (3-D-QSAR) models, using comparative molecular field analysis (CoMFA) and comparative similarity indices analysis (CoMSIA), were built based on calculated structural indices and a reported experimental toxicology index (aryl hydrocarbon receptor relative binding affinities, RBA) of 18 PBDEs congeners, to determine the factors required for the RBA of these PBDEs. After performing leave-one-out cross-validation, satisfactory results were obtained with cross-validation O2 and R2 values of 0.580 and 0.995 by the CoMFA model and 0.680 and 0.982 by the CoMSIA model, respectively. The results showed clearly that the nonplanar conformations of PBDEs result in the lowest energy level and that the electrostatic index was the main factor reflecting the RBA of PBDEs. The two QSAR models were then used to predict the RBA value of 46 PBDEs for which experimental values are unavailable at present. PMID:16053097

  16. 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.

  17. Quantitative structure-activity relationships for the mutagenicity of propylene oxides with Salmonella.

    PubMed

    Hooberman, B H; Chakraborty, P K; Sinsheimer, J E

    1993-04-01

    A quantitative structure-activity relationship approach was used to investigate the mutagenicity of a series of seventeen-monosubstituted propylene oxides in Salmonella typhimurium strains TA100 and TA1535. Mutagenicity in strain TA100, using a liquid suspension assay, was found to correlate with chemical reactivity, as measured by the rates of reaction with two model bionucleophiles, nicotinamide and 4-(4-nitrobenzyl)pyridine. However, since the reactivity of three of the epoxides did not correlate to their Taft sigma * values, as a measure of the electronic effects of substituent groups, neither was their mutagenicity predicted by this substituent constant. The relative mutagenicity for the propylene oxides was different in the liquid suspension assay than that determined by the standard plate incorporation assay and also differed between the two bacterial strains. The assay differences were attributed to epoxide stability. The differences between strains was observed to be due to the response of the error-prone repair system, found only in TA100, to the stronger alkylating agents. PMID:7680427

  18. 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.

  19. 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

  20. Determination of microsomal lauric acid hydroxylase activity by HPLC with flow-through radiochemical quantitation

    SciTech Connect

    Romano, M.C.; Straub, K.M.; Yodis, L.A.P.; Eckardt, R.D.; Newton, J.F.

    1988-04-01

    An assay for the microsomal hydroxylation of lauric acid (LA), based on HPLC with flow-through radiochemical detection, has been developed. Conditions were optimized for resolution and quantitation of three microsomal metabolites of /sup 14/C-LA, one of which has not been reported previously as a metabolite of LA in mammalian microsomal incubations. These products, 12-(omega)-hydroxy-LA, 11-(omega-1)-hydroxy-LA, and a novel metabolite, 10-(omega-2)-hydroxy-LA, were isolated by HPLC and identified by gas chromatography/mass spectrometry. In the presence of NADPH, the formation of all three metabolites was linear with time and microsomal protein concentration. Hydrogen peroxide also supported the microsomal metabolism of LA, although the ratio of metabolites was substantially different than that produced by NADPH-supported microsomes. Several biochemical probes (metyrapone, ..cap alpha..-naphthoflavone, 2-diethylaminoethyl-2,2-diphenylvalerate hydrochloride, and 10-undecynoic acid) were used to dissociate the three LA hydroxylase activities. These experiments suggest that the site-specific hydroxylation (omega-, (omega-1), (omega-2)-) of LA may be catalyzed by different isozymes of cytochrome P-450.

  1. Sensitivity Analyses of Exposure Estimates from a Quantitative Job-exposure Matrix (SYN-JEM) for Use in Community-based Studies

    PubMed Central

    Peters, Susan

    2013-01-01

    Objectives: We describe the elaboration and sensitivity analyses of a quantitative job-exposure matrix (SYN-JEM) for respirable crystalline silica (RCS). The aim was to gain insight into the robustness of the SYN-JEM RCS estimates based on critical decisions taken in the elaboration process. Methods: SYN-JEM for RCS exposure consists of three axes (job, region, and year) based on estimates derived from a previously developed statistical model. To elaborate SYN-JEM, several decisions were taken: i.e. the application of (i) a single time trend; (ii) region-specific adjustments in RCS exposure; and (iii) a prior job-specific exposure level (by the semi-quantitative DOM-JEM), with an override of 0 mg/m3 for jobs a priori defined as non-exposed. Furthermore, we assumed that exposure levels reached a ceiling in 1960 and remained constant prior to this date. We applied SYN-JEM to the occupational histories of subjects from a large international pooled community-based case–control study. Cumulative exposure levels derived with SYN-JEM were compared with those from alternative models, described by Pearson correlation (Rp) and differences in unit of exposure (mg/m3-year). Alternative models concerned changes in application of job- and region-specific estimates and exposure ceiling, and omitting the a priori exposure ranking. Results: Cumulative exposure levels for the study subjects ranged from 0.01 to 60 mg/m3-years, with a median of 1.76 mg/m3-years. Exposure levels derived from SYN-JEM and alternative models were overall highly correlated (Rp > 0.90), although somewhat lower when omitting the region estimate (Rp = 0.80) or not taking into account the assigned semi-quantitative exposure level (Rp = 0.65). Modification of the time trend (i.e. exposure ceiling at 1950 or 1970, or assuming a decline before 1960) caused the largest changes in absolute exposure levels (26–33% difference), but without changing the relative ranking (Rp = 0.99). Conclusions: Exposure estimates

  2. Using an Active Sensor to Estimate Orchard Grass (Dactylis glomerata L.) Dry Matter Yield and Quality

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Remote sensing in the form of active sensors could be used to estimate forage biomass on spatial and temporal scales. The objective of this study is to use canopy reflectance measurements from an active remote sensor to compare different vegetation indices as a means of estimating final dry matter y...

  3. 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.

  4. Toward a class-independent quantitative structure--activity relationship model for uncouplers of oxidative phosphorylation.

    PubMed

    Spycher, Simon; Smejtek, Pavel; Netzeva, Tatiana I; Escher, Beate I

    2008-04-01

    A mechanistically based quantitative structure-activity relationship (QSAR) for the uncoupling activity of weak organic acids has been derived. The analysis of earlier experimental studies suggested that the limiting step in the uncoupling process is the rate with which anions can cross the membrane and that this rate is determined by the height of the energy barrier encountered in the hydrophobic membrane core. We use this mechanistic understanding to develop a predictive model for uncoupling. The translocation rate constants of anions correlate well with the free energy difference between the energy well and the energy barrier, Delta G well-barrier,A (-) , in the membrane calculated by a novel approach to describe internal partitioning in the membrane. An existing data set of 21 phenols measured in an in vitro test system specific for uncouplers was extended by 14 highly diverse compounds. A simple regression model based on the experimental membrane-water partition coefficient and Delta G well-barrier,A (-) showed good predictive power and had meaningful regression coefficients. To establish uncoupler QSARs independent of chemical class, it is necessary to calculate the descriptors for the charged species, as the analogous descriptors of the neutral species showed almost no correlation with the translocation rate constants of anions. The substitution of experimental with calculated partition coefficients resulted in a decrease of the model fit. A particular strength of the current model is the accurate calculation of excess toxicity, which makes it a suitable tool for database screening. The applicability domain, limitations of the model, and ideas for future research are critically discussed. PMID:18358007

  5. 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

    Melchinger, A E; Utz, H F; Schön, C C

    1998-05-01

    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

  6. Comprehensive Energetic Scale for Quantitatively Estimating the Fluorinating Potential of N-F Reagents in Electrophilic Fluorinations.

    PubMed

    Xue, Xiao-Song; Wang, Ya; Li, Man; Cheng, Jin-Pei

    2016-05-20

    Quantitative knowledge of the fluorinating strength of electrophilic N-F reagents is of crucial importance for rational design and optimization of novel reagents and new reactions. Herein, we report the first systematic computation of fluorinating potentials of 130 electrophilic N-F reagents in two commonly used solvents dichloromethane and acetonitrile in terms of the N-F bond heterolysis energies as expressed by the fluorine plus detachment (FPD) values. The calculated FPD scales of 130 N-F reagents cover a range from 112.3 to 290.4 kcal mol(-1) and 110.9 to 278.4 kcal mol(-1) in dichloromethane and acetonitrile, respectively. This comprehensive FPD database provides a valuable quantitative guide for studying the influence of structural variation on the fluorinating strength of the N-F reagents, opening a door to the rational design of novel reagents with appropriate fluorinating strength for specific purposes. It is demonstrated that the FPD values can reproduce the reactivity order for electrophilic N-F reagents better than other parameters. PMID:27120313

  7. 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…

  8. 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…

  9. Peroxisome induction potential and lipid-regulating activity in rats. Quantitative microscopy and chemical structure-activity relationships.

    PubMed Central

    McGuire, E. J.; Lucas, J. A.; Gray, R. H.; de la Iglesia, F. A.

    1991-01-01

    Structurally diverse lipid-regulating agents induce hepatomegaly, hepatic peroxisome proliferation, and hepatocarcinoma in rats by mechanisms not fully understood. Nevertheless the initial hepatic response is a prompt, florid proliferation of peroxisomes. In investigations reported here, changes in the rat hepatic peroxisome compartment were measured by quantitative microscopy to determine chemical structure requirements that relate to peroxisome proliferation and lipid regulation. Aryloxyalkanoic acids plus amide analogs, and thio, benzimidazole, phenylpiperazine, and oxazole derivatives induced peroxisome proliferation and generally decreased plasma triglyceride and total cholesterol levels. These compounds contain an acidic function or are readily metabolized to a chemical with an acidic function. Substitution of the acidic function with an adamantyloxy eliminated peroxisome proliferation and induced contrasting effects on lipid profile, increasing triglycerides and decreasing total cholesterol. A previously unreported, direct correlation emerged between peroxisome proliferation and plasma high-density lipoprotein-cholesterol levels. These effects could not be elicited separately, negating identification of functional groups that could be associated with either activity. Chemical structure and resulting peroxisome proliferation with changes in plasma lipoproteins are therefore closely interrelated in rats. Images Figure 1 PMID:1853935

  10. 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

  11. 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 ...

  12. 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

  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). PMID:25891081

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. QUANTITATIVE COMPARISON OF MOLECULAR ELECTROSTATIC POTENTIALS FOR STRUCTURE-ACTIVITY STUDIES

    EPA Science Inventory

    Further development of an approach for representing, efficiently calculating and comparing discreet 3-dimensional molecular electrostatic potentials using a quantitative similarity index (MEP-SI) based on the Carbo formalism is presented. adial-type (MACRA) grid representation is...

  19. Quantitative structure-activity relationships (QSARs) using the novel marine algal toxicity data of phenols.

    PubMed

    Ertürk, M Doğa; Saçan, Melek Türker; Novic, Marjana; Minovski, Nikola

    2012-09-01

    The present study reports for the first time in its entirety the toxicity of 30 phenolic compounds to marine alga Dunaliella tertiolecta. Toxicity of polar narcotics and respiratory uncouplers was strongly correlated to hydrophobicity as described by the logarithm of the octanol/water partition coefficient (Log P). Compounds expected to act by more reactive mechanisms, particularly hydroquinones, were shown to have toxicity in excess of that predicted by Log P. A quality quantitative structure-activity relationship (QSAR) was obtained with Log P and a 2D autocorrelation descriptor weighted by atomic polarizability (MATS3p) only after the removal of hydroquinones from the data set. In an attempt to model the whole data set including hydroquinones, 3D descriptors were included in the modeling process and three quality QSARs were developed using multiple linear regression (MLR). One of the most significant results of the present study was the superior performance of the consensus MLR model, obtained by averaging the predictions from each individual linear model, which provided excellent prediction accuracy for the test set (Q(test)²=0.94). The four-parameter Counter Propagation Artificial Neural Network (CP ANN) model, which was constructed using four out of six descriptors that appeared in the linear models, also provided an excellent external predictivity (Q(test)²=0.93). The proposed algal QSARs were further tested in their predictivity using an external set comprising toxicity data of 44 chemicals on freshwater alga Pseudokirchneriella subcapitata. The two-parameter global model employing a 3D descriptor (Mor24m) and a charge-related descriptor (C(ortho)) not only had high external predictivity (Q(ext)²=0.74), but it also had excellent external data set coverage (%97). PMID:23085159

  20. Quantitative structure activity relationship and risk analysis of some pesticides in the goat milk.

    PubMed

    Muhammad, Faqir; Awais, Mian Muhammad; Akhtar, Masood; Anwar, Muhammad Irfan

    2013-01-01

    The detection and quantification of different pesticides in the goat milk samples collected from different localities of Faisalabad, Pakistan was performed by HPLC using solid phase microextraction. The analysis showed that about 50% milk samples were contaminated with pesticides. The mean±SEM levels (ppm) of cyhalothrin, endosulfan, chlorpyrifos and cypermethrin were 0.34±0.007, 0.063±0.002, 0.034±0.002 and 0.092±0.002, respectively; whereas, methyl parathion was not detected in any of the analyzed samples. Quantitative structure activity relationship (QSAR) models were suggested to predict the residues of unknown pesticides in the goat milk using their known physicochemical characteristics including molecular weight (MW), melting point (MP), and log octanol to water partition coefficient (Ko/w) in relation to the characteristics such as pH, % fat, specific gravity and refractive index of goat milk. The analysis revealed good correlation coefficient (R2 = 0.985) for goat QSAR model. The coefficients for Ko/w and refractive index for the studied pesticides were higher in goat milk. This suggests that these are better determinants for pesticide residue prediction in the milk of these animals. Based upon the determined pesticide residues and their provisional tolerable daily intakes, risk analysis was also conducted which showed that daily intake levels of pesticide residues including cyhalothrin, chlorpyrifos and cypermethrin in present study are 2.68, 5.19 and 2.71 times higher, respectively in the goat milk. This intake of pesticide contaminated milk might pose health hazards to humans in this locality. PMID:23369514

  1. Quantitative structure–activity relationship analysis of the pharmacology of para-substituted methcathinone analogues

    PubMed Central

    Bonano, J S; Banks, M L; Kolanos, R; Sakloth, F; Barnier, M L; Glennon, R A; Cozzi, N V; Partilla, J S; Baumann, M H; Negus, S S

    2015-01-01

    Background and Purpose Methcathinone (MCAT) is a potent monoamine releaser and parent compound to emerging drugs of abuse including mephedrone (4-CH3 MCAT), the para-methyl analogue of MCAT. This study examined quantitative structure–activity relationships (QSAR) for MCAT and six para-substituted MCAT analogues on (a) in vitro potency to promote monoamine release via dopamine and serotonin transporters (DAT and SERT, respectively), and (b) in vivo modulation of intracranial self-stimulation (ICSS), a behavioural procedure used to evaluate abuse potential. Neurochemical and behavioural effects were correlated with steric (Es), electronic (σp) and lipophilic (πp) parameters of the para substituents. Experimental Approach For neurochemical studies, drug effects on monoamine release through DAT and SERT were evaluated in rat brain synaptosomes. For behavioural studies, drug effects were tested in male Sprague-Dawley rats implanted with electrodes targeting the medial forebrain bundle and trained to lever-press for electrical brain stimulation. Key Results MCAT and all six para-substituted analogues increased monoamine release via DAT and SERT and dose- and time-dependently modulated ICSS. In vitro selectivity for DAT versus SERT correlated with in vivo efficacy to produce abuse-related ICSS facilitation. In addition, the Es values of the para substituents correlated with both selectivity for DAT versus SERT and magnitude of ICSS facilitation. Conclusions and Implications Selectivity for DAT versus SERT in vitro is a key determinant of abuse-related ICSS facilitation by these MCAT analogues, and steric aspects of the para substituent of the MCAT scaffold (indicated by Es) are key determinants of this selectivity. PMID:25438806

  2. Quantitative structure activity relationship and risk analysis of some pesticides in the goat milk

    PubMed Central

    2013-01-01

    The detection and quantification of different pesticides in the goat milk samples collected from different localities of Faisalabad, Pakistan was performed by HPLC using solid phase microextraction. The analysis showed that about 50% milk samples were contaminated with pesticides. The mean±SEM levels (ppm) of cyhalothrin, endosulfan, chlorpyrifos and cypermethrin were 0.34±0.007, 0.063±0.002, 0.034±0.002 and 0.092±0.002, respectively; whereas, methyl parathion was not detected in any of the analyzed samples. Quantitative structure activity relationship (QSAR) models were suggested to predict the residues of unknown pesticides in the goat milk using their known physicochemical characteristics including molecular weight (MW), melting point (MP), and log octanol to water partition coefficient (Ko/w) in relation to the characteristics such as pH, % fat, specific gravity and refractive index of goat milk. The analysis revealed good correlation coefficient (R2 = 0.985) for goat QSAR model. The coefficients for Ko/w and refractive index for the studied pesticides were higher in goat milk. This suggests that these are better determinants for pesticide residue prediction in the milk of these animals. Based upon the determined pesticide residues and their provisional tolerable daily intakes, risk analysis was also conducted which showed that daily intake levels of pesticide residues including cyhalothrin, chlorpyrifos and cypermethrin in present study are 2.68, 5.19 and 2.71 times higher, respectively in the goat milk. This intake of pesticide contaminated milk might pose health hazards to humans in this locality. PMID:23369514

  3. 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

  4. Quantitative structure-activity analysis of the algae toxicity of nitroaromatic compounds.

    PubMed

    Schmitt, H; Altenburger, R; Jastorff, B; Schüürmann, G

    2000-06-01

    Proliferation toxicity toward the algae Scenedesmus vacuolatus in a 24 h one-generation reproduction assay was determined for nitrobenzene and 18 derivatives, including two phenols. The resultant EC(50) values covering more than 4 orders of magnitude were subjected to a quantitative structure-activity analysis (QSAR) using hydrophobicity in terms of the octanol/water partition coefficient in logarithmic form, log K(ow), and 16 quantum chemical descriptors of molecular reactivity that were calculated with the AM1 scheme. For 13 mononitro derivatives and the highly hydrophobic trifluralin, a narcotic-type mode of action can explain most of the toxicity variation. Correction of log K(ow) for ionization for the phenols and quantification of the molecular susceptibility for one-electron reduction as apparently rate-determining biotransformation step by the energy of the lowest unoccupied molecular orbital, E(LUMO), yields a highly significant QSAR for all 19 compounds (r(adj)(2) = 0.90), which can be further improved when adding the maximum net atomic charge at the nitro nitrogen, q(nitro)(-)(N), as the third descriptor (r(adj)(2) = 0.93). Comparison of the energy of the singly occupied molecular orbital, E(SOMO), of the radical anions as initial metabolites with the E(SOMO) of known redox cyclers suggests that dinitrobenzenes and TFM as well as multiply chlorinated nitrobenzenes may also exert oxidative stress. This is based on an E(SOMO) window of -0.30 to 0. 55 eV as a tentative criterion for molecular structures to have the potential for redox cycling, derived from a set of eight known redox cyclers. The discussion includes a detailed analysis of apparently relevant metabolic pathways and associated modes of toxic action of nitroaromatics. PMID:10858317

  5. Multiobjective optimization in quantitative structure-activity relationships: deriving accurate and interpretable QSARs.

    PubMed

    Nicolotti, Orazio; Gillet, Valerie J; Fleming, Peter J; Green, Darren V S

    2002-11-01

    Deriving quantitative structure-activity relationship (QSAR) models that are accurate, reliable, and easily interpretable is a difficult task. In this study, two new methods have been developed that aim to find useful QSAR models that represent an appropriate balance between model accuracy and complexity. Both methods are based on genetic programming (GP). The first method, referred to as genetic QSAR (or GPQSAR), uses a penalty function to control model complexity. GPQSAR is designed to derive a single linear model that represents an appropriate balance between the variance and the number of descriptors selected for the model. The second method, referred to as multiobjective genetic QSAR (MoQSAR), is based on multiobjective GP and represents a new way of thinking of QSAR. Specifically, QSAR is considered as a multiobjective optimization problem that comprises a number of competitive objectives. Typical objectives include model fitting, the total number of terms, and the occurrence of nonlinear terms. MoQSAR results in a family of equivalent QSAR models where each QSAR represents a different tradeoff in the objectives. A practical consideration often overlooked in QSAR studies is the need for the model to promote an understanding of the biochemical response under investigation. To accomplish this, chemically intuitive descriptors are needed but do not always give rise to statistically robust models. This problem is addressed by the addition of a further objective, called chemical desirability, that aims to reward models that consist of descriptors that are easily interpretable by chemists. GPQSAR and MoQSAR have been tested on various data sets including the Selwood data set and two different solubility data sets. The study demonstrates that the MoQSAR method is able to find models that are at least as good as models derived using standard statistical approaches and also yields models that allow a medicinal chemist to trade statistical robustness for chemical

  6. 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

  7. 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.

  8. Rat- and human-based risk estimates of lung cancer from occupational exposure to poorly-soluble particles: A quantitative evaluation

    NASA Astrophysics Data System (ADS)

    Kuempel, E. D.; Smith, R. J.; Dankovic, D. A.; Stayner, L. T.

    2009-02-01

    In risk assessment there is a need for quantitative evaluation of the capability of animal models to predict disease risks in humans. In this paper, we compare the rat- and human-based excess risk estimates for lung cancer from working lifetime exposures to inhaled poorly-soluble particles. The particles evaluated include those for which long-term dose-response data are available in both species, i.e., coal dust, carbon black, titanium dioxide, silica, and diesel exhaust particulate. The excess risk estimates derived from the rat data were generally lower than those derived from the human studies, and none of the rat- and human-based risk estimates were significantly different (all p-values>0.05). Residual uncertainty in whether the rat-based risk estimates would over- or under-predict the true excess risks of lung cancer from inhaled poorly-soluble particles in humans is due in part to the low power of the available human studies, limited particle size exposure data for humans, and ambiguity about the best animal models and extrapolation methods.

  9. Quantitative estimates of Mid- to late Holocene Climate Variability in northeastern Siberia inferred from chironomids in lake sediments

    NASA Astrophysics Data System (ADS)

    Nazarova, Larisa; Diekmann, Bernhard; Pestrjakova, Ludmila; Herzschuh, Ulrike; Subetto, Dmitry

    2010-05-01

    Yakutia (Russia, northeastern part of Eurasia) represents one of Earths most extreme climatic settings in the world with deep-reaching frozen ground and a semiarid continental climate with highest seasonal temperature contrasts in the northern hemisphere. The amplitude of temperature variations around the year sometimes exceeds 100oC. There are few examples of quantitative palaeoecological studies in Siberia and these data have to be tested by quantitative studies from other sites in this region, inferred from different proxies and using regional calibration datasets and temperature models that are still lacking. Chironomid midges (Insecta, Diptera, Chironomidae) have been widely used to reconstruct past climate variability in many areas of Western Europe and North America. A chironomid-mean July air temperature inference model has been developed, based on a modern calibration set of 200 lakes sampled along a transect from 110° to 159° E and 61° to73° N in northern Russia. The inference model was applied to sediment cores from 2 lakes in the Central Yakutia in order to reconstruct past July air temperatures. The lacustrine records span mid- to late Holocene. The downcore variability in the chironomid assemblages and the composition of organic matter give evidence of climate-driven and interrelated changes in biological productivity, lacustrine trophic states, and lake-level fluctuations. Three phases of the climate development in Central Yakutia can be derived from the geochemical composition of the lake cores and according to the inferred from chironomid assemblages mean July air ToC. Content of organic matters reached maximal values in the period between 7000-4500 yBP. Sedimentation rate is especially high, numerous molluscs shells are found in sediments. All this along with the reconstructed air temperature confirmed that Mid Holocene optimum in Central Yakutia took place in this period with the maximal temperatures up to 4oC above present day ToC. Strong

  10. Quantitative estimation of Hyblaea puera NPV production in three larval stages of the teak defoliator, Hyblaea puera (Cramer).

    PubMed

    Biji, C P; Sudheendrakumar, V V; Sajeev, T V

    2006-09-01

    Hyblaea puera nucleoployhedrovirus (HpNPV) is a potential biocontrol agent of the teak defoliator, Hyblaea puera (Cramer) (Lepidoptera: Hyblaeidae). To quantify the growth of the virus in the host larvae, three larval stages of the teak defoliator were subjected to quantitative bioassays using specified dilutions of HpNPV. The HpNPV production was found to be dependent on the dose, incubation period as well as stage specific responses of the host insect used. As larvae matured, production of the virus per mg body weight was not found to be in a constant proportion to the increase in the body weight. The combination which yielded the greatest virus production of 3.55 x 10(9) polyhedral occlusion bodies (POBs) was that in which larva weighing 26-37 mg was fed with 1 x 10(6) POBs, incubated for 6 h and harvested at 72 h post infection (h p.i.). The response of the fourth instar larvae was found to be more productive than the third and fifth instar larvae, which makes it an ideal candidate for mass production of the virus in vivo. PMID:16687178

  11. 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

  12. 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…

  13. 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…

  14. 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.

  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. Quantitative testing of the methodology for genome size estimation in plants using flow cytometry: a case study of the Primulina genus

    PubMed Central

    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. PMID:26042140

  17. 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...

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. 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

  3. 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

  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. PMID:26773437

  5. Anatomical and Functional Estimations of Brachial Artery Diameter and Elasticity Using Oscillometric Measurements with a Quantitative Approach

    PubMed Central

    Yoshinaga, Keiichiro; Fujii, Satoshi; Tomiyama, Yuuki; Takeuchi, Keisuke; Tamaki, Nagara

    2016-01-01

    Noninvasive vascular function measurement plays an important role in detecting early stages of atherosclerosis and in evaluating therapeutic responses. In this regard, recently, new vascular function measurements have been developed. These new measurements have been used to evaluate vascular function in coronary arteries, large aortic arteries, or peripheral arteries. Increasing vascular diameter represents vascular remodeling related to atherosclerosis. Attenuated vascular elasticity may be a reliable marker for atherosclerotic risk assessment. However, previous measurements for vascular diameter and vascular elasticity have been complex, operator-dependent, or invasive. Therefore, simple and reliable approaches have been sought. We recently developed a new automated oscillometric method to measure the estimated area (eA) of a brachial artery and its volume elastic modulus (VE). In this review, we further report on this new measurement and other vascular measurements. We report on the reliability of the new automated oscillometric measurement of eA and VE. Based on our findings, this measurement technique should be a reliable approach, and this modality may have practical application to automatically assess muscular artery diameter and elasticity in clinical or epidemiological settings. In this review, we report the characteristics of our new oscillometric measurements and other related vascular function measurements. PMID:27493898

  6. 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.

  7. Development and Validation of an RP-HPLC Method for Quantitative Estimation of Eslicarbazepine Acetate in Bulk Drug and Tablets

    PubMed Central

    Singh, M.; Kumar, L.; Arora, P.; Mathur, S. C.; Saini, P. K.; Singh, R. M.; Singh, G. N.

    2013-01-01

    A convenient, simple, accurate, precise and reproducible RP-HPLC method was developed and validated for the estimation of eslicarbazepine acetate in bulk drug and tablet dosage form. Objective was achieved under optimised chromatographic conditions on Dionex RP-HPLC system with Dionex C18 column (250×4.6 mm, 5 μm particle size) using mobile phase composed of methanol and ammonium acetate (0.005 M) in the ratio of 70:30 v/v. The separation was achieved using an isocratic elution method with a flow rate of 1.0 ml/ min at room temperature. The effluent was monitored at 230 nm using diode array detector. The retention time of eslicarbazepine acetate is found to be 4.9 min and the standard calibration plot was linear over a concentration range of 10-90 μg/ml with r2=0.9995. The limit of detection and quantification were found to be 3.144 and 9.52 μg/ml, respectively. The amount of eslicarbazepine acetate in bulk and tablet dosage form was found to be 99.19 and 97.88%, respectively. The method was validated statistically using the percent relative standard deviation and the values are found to be within the limits. The recovery studies were performed and the percentage recoveries were found to be 98.33± 0.5%. PMID:24591752

  8. Development and Validation of an RP-HPLC Method for Quantitative Estimation of Eslicarbazepine Acetate in Bulk Drug and Tablets.

    PubMed

    Singh, M; Kumar, L; Arora, P; Mathur, S C; Saini, P K; Singh, R M; Singh, G N

    2013-11-01

    A convenient, simple, accurate, precise and reproducible RP-HPLC method was developed and validated for the estimation of eslicarbazepine acetate in bulk drug and tablet dosage form. Objective was achieved under optimised chromatographic conditions on Dionex RP-HPLC system with Dionex C18 column (250×4.6 mm, 5 μm particle size) using mobile phase composed of methanol and ammonium acetate (0.005 M) in the ratio of 70:30 v/v. The separation was achieved using an isocratic elution method with a flow rate of 1.0 ml/ min at room temperature. The effluent was monitored at 230 nm using diode array detector. The retention time of eslicarbazepine acetate is found to be 4.9 min and the standard calibration plot was linear over a concentration range of 10-90 μg/ml with r(2)=0.9995. The limit of detection and quantification were found to be 3.144 and 9.52 μg/ml, respectively. The amount of eslicarbazepine acetate in bulk and tablet dosage form was found to be 99.19 and 97.88%, respectively. The method was validated statistically using the percent relative standard deviation and the values are found to be within the limits. The recovery studies were performed and the percentage recoveries were found to be 98.33± 0.5%. PMID:24591752

  9. 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

  10. 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.

  11. 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

  12. 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

  13. The Role of Hemispheral Asymmetry and Regional Activity of Quantitative EEG in Children with Stuttering

    ERIC Educational Resources Information Center

    Ozge, Aynur; Toros, Fevziye; Comelekoglu, Ulku

    2004-01-01

    We investigated the role of delayed cerebral maturation, hemisphere asymmetry and regional differences in children with stuttering and healthy controls during resting state and hyperventilation, using conventional EEG techniques and quantitative EEG (QEEG) analysis. This cross-sectional case control study included 26 children with stuttering and…

  14. Quantitative Assessment of Disinfectant Activity Against Listeria monocytogenes Biofilms Under Flow Conditions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Listeria monocytogenes has a high mortality in humans and is responsible for most food recalls involving bacterial contamination. Our objective was to develop methods to quantitatively assess the pathogen under flow conditions to mimic wet food processing. A reactor was used to grow the bacteria on ...

  15. Effects of Drawing on Alpha Activity: A Quantitative EEG Study with Implications for Art Therapy

    ERIC Educational Resources Information Center

    Belkofer, Christopher M.; Van Hecke, Amy Vaughan; Konopka, Lukasz M.

    2014-01-01

    Little empirical evidence exists as to how materials used in art therapy affect the brain and its neurobiological functioning. This pre/post within-groups study utilized the quantitative electroencephalogram (qEEG) to measure residual effects in the brain after 20 minutes of drawing. EEG recordings were conducted before and after participants (N =…

  16. 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

  17. 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.

  18. Quantitative and rapid estimations of human sub-surface skin mass using ultra-high-resolution spectral domain optical coherence tomography.

    PubMed

    Kuo, Wen-Chuan; Kuo, Yue-Ming; Wen, Su-Ying

    2016-04-01

    Non-invasive and quantitative estimations for the delineation of sub-surface tumor margins could greatly aid in the early detection and monitoring of the morphological appearances of tumor growth, ensure complete tumor excision without the unnecessary sacrifice of healthy tissue, and facilitate post-operative follow-up for recurrence. In this study, a high-speed, non-invasive, and ultra-high-resolution spectral domain optical coherence tomography (UHR-SDOCT) imaging platform was developed for the quantitative measurement of human sub-surface skin mass. With a proposed robust, semi-automatic analysis, the system can rapidly quantify lesion area and shape regularity by an en-face-oriented algorithm. Various sizes of nylon sutures embedded in pork skin were used first as a phantom to verify the accuracy of our algorithm, and then in vivo, feasibility was proven using benign human angiomas and pigmented nevi. Clinically, this is the first step towards an automated skin lesion measurement system. In vivo optical coherence tomography (OCT) image of angioma (A). Thin red arrows point to a blood vessel (BV). PMID:25755214

  19. 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

  20. 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

  1. Uptake and recycling of lead by boreal forest plants: Quantitative estimates from a site in northern Sweden

    NASA Astrophysics Data System (ADS)

    Klaminder, Jonatan; Bindler, Richard; Emteryd, Ove; Renberg, Ingemar

    2005-05-01

    As a consequence of deposition of atmospheric pollution, the lead concentration in the mor layer (the organic horizon) of remote boreal forest soils in Sweden is raised far above natural levels. How the mor will respond to decreased atmospheric pollution is not well known and is dependent on future deposition rates, downward migration losses and upward fluxes in the soil profile. Plants may contribute to the upward flux of lead by 'pumping' lead back to the mor surface through root uptake and subsequent litter fall. We use lead concentration and stable isotope ( 206Pb, 207Pb and 208Pb) measurements of forest vegetation to quantify plant uptake rates from the soil and direct from the atmosphere at two sites in northern Sweden; an undisturbed mature forest and a disturbed site with Scots pine ( Pinus sylvestris) growing on a recently exposed mineral soil (C-horizon) containing a minimum of atmospherically derived pollution lead. Analyses of forest mosses from a herbarium collection (spanning the last ˜100 yr) and soil matrix samples suggest that the atmospheric lead deposited on plants and soil has an average 206Pb/ 207Pb ratio of 1.15, while lead derived from local soil minerals has an average ratio of ˜1.47. Since the biomass of trees and field layer shrubs has an average 206Pb/ 207Pb ratio of ˜1.25, this indicates that 70% ± 10% of the inventory of 1 ± 0.8 mg Pb m -2 stored in plants in the mature forest originates from pollution. Needles, bark and apical stemwood of the pine growing on the disturbed soil, show lower 206Pb/ 207Pb ratios (as low as 1.21) than the roots and basal stemwood (having ratios > 1.36), which indicate that plants are able to incorporate lead directly from the atmosphere (˜50% of the total tree uptake). By partitioning the total uptake of lead into uptake from the atmosphere and different soil layers using an isotopic mixing model, we estimate that ˜0.03 ± 0.01, 0.02 ± 0.01 and 0.05 ± 0.01 mg Pb m -2 yr -1 (mean ± SD), is taken up

  2. 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 ETS activity as an estimator of thermal tolerance at the mitochondrial level and PGS as an indicator of thermal tolerance at the organismic level showed the shift of optimum temperature ranges of ETS activity to the right for 2° in O. limosus and for 3° in P. leniusculus. Thus, lower estimated temperature optima and temperatures of optimum ranges of PGS compared to ETS activity could indicate higher thermal sensitivity at the organismic level than at a lower level of complexity (i.e. at the mitochondrial level). The response of ETS activity to temperature change, especially at lower and higher temperatures, indicates differences in the characteristics of the ETSs in O. limosus and P. leniusculus. O. limosus is less sensitive to high temperature. The significant correlation between PGS and ETS activity supports our assumption that ETS activity could be used for the rapid estimation of thermal tolerance in crayfish species. PMID:24679968

  3. Usefulness of graphical invariants in quantitative structure-activity correlations of tuberculostatic drugs of the isonicotinic acid hydrazide type.

    PubMed

    Bagchi, Manish C; Maiti, Bhim C; Mills, Denise; Basak, Subhash C

    2004-04-01

    Quantitative structure-activity relationship (QSAR) studies have been performed for a series of 2-substituted isonicotinic acid hydrazides utilizing theoretical molecular descriptors. 223 topological (topostructural and topochemical) indices along with seven geometrical descriptors were computed for the prediction of antibacterial activity against Mycobacterium tuberculosis. Ridge-regression models assessed by cross-validated R2 have been formulated, and a comparative study on the relative effectiveness of physicochemical vis-à-vis theoretical molecular descriptors performed. The models developed clearly indicate the supremacy of structure-activity over property-activity relationships in the current study and can be used to evaluate the potential tuberculostatic activity of other INH derivatives, real or hypothetical. PMID:14691675

  4. Low cost quantitative digital imaging as an alternative to qualitative in vivo bioassays for analysis of active aflatoxin B1.

    PubMed

    Rasooly, Reuven; Do, Paula M; Hernlem, Bradley J

    2016-06-15

    Aflatoxin B1 (AFB1) producing fungi contaminate food and feed and are a major health concern. To minimize the sources and incidence of AFB1 illness there is a need to develop affordable, sensitive mobile devices for detection of active AFB1. In the present study we used a low cost fluorescence detector and describe two quantitative assays for detection of detoxified and active AFB1 demonstrating that AFB1 concentration can be measured as intensity of fluorescence. When the assay plate containing increasing concentrations of AFB1 is illuminated with a 366 nm ultraviolet lamp, AFB1 molecules absorb photons and emit blue light with peak wavelength of 432 nm. The fluorescence intensity increased in dose dependent manner. However, this method cannot distinguish between active AFB1 which poses a threat to health, and the detoxified AFB1 which exhibits no toxicity. To measure the toxin activity, we used a cell based assay that makes quantification more robust and is capable of detecting multiple samples simultaneously. It is an alternative to the qualitative duckling bioassay which is the "gold-standard" assay currently being used for quantitative analysis of active AFB1. AFB1 was incubated with transduced Vero cells expressing the green fluorescence protein (GFP) gene. After excitation with blue light at 475 nm, cells emitted green light with emission peak at 509 nm. The result shows that AFB1 inhibits protein expression in a concentration dependent manner resulting in proportionately less GFP fluorescence in cells exposed to AFB1. The result also indicates strong positive linear relationship with R(2)=0.90 between the low cost CCD camera and a fluorometer, which costs 100 times more than a CCD camera. This new analytical method for measuring active AFB1 is low in cost and combined with in vitro assay, is quantitative. It also does not require the use of animals and may be useful especially for laboratories in regions with limited resources. PMID:26874107

  5. Ecosystem services - from assessements of estimations to quantitative, validated, high-resolution, continental-scale mapping via airborne LIDAR

    NASA Astrophysics Data System (ADS)

    Zlinszky, András; Pfeifer, Norbert

    2016-04-01

    service potential" which is the ability of the local ecosystem to deliver various functions (water retention, carbon storage etc.), but can't quantify how much of these are actually used by humans or what the estimated monetary value is. Due to its ability to measure both terrain relief and vegetation structure in high resolution, airborne LIDAR supports direct quantification of the properties of an ecosystem that lead to it delivering a given service (such as biomass, water retention, micro-climate regulation or habitat diversity). In addition, its high resolution allows direct calibration with field measurements: routine harvesting-based ecological measurements, local biodiversity indicator surveys or microclimate recordings all take place at the human scale and can be directly linked to the local value of LIDAR-based indicators at meter resolution. Therefore, if some field measurements with standard ecological methods are performed on site, the accuracy of LIDAR-based ecosystem service indicators can be rigorously validated. With this conceptual and technical approach high resolution ecosystem service assessments can be made with well established credibility. These would consolidate the concept of ecosystem services and support both scientific research and evidence-based environmental policy at local and - as data coverage is continually increasing - continental scale.

  6. Development of pharmacophore similarity-based quantitative activity hypothesis and its applicability domain: applied on a diverse data-set of HIV-1 integrase inhibitors.

    PubMed

    Kumar, Sivakumar Prasanth; Jasrai, Yogesh T; Mehta, Vijay P; Pandya, Himanshu A

    2015-01-01

    Quantitative pharmacophore hypothesis combines the 3D spatial arrangement of pharmacophore features with biological activities of the ligand data-set and predicts the activities of geometrically and/or pharmacophoric similar ligands. Most pharmacophore discovery programs face difficulties in conformational flexibility, molecular alignment, pharmacophore features sampling, and feature selection to score models if the data-set constitutes diverse ligands. Towards this focus, we describe a ligand-based computational procedure to introduce flexibility in aligning the small molecules and generating a pharmacophore hypothesis without geometrical constraints to define pharmacophore space, enriched with chemical features necessary to elucidate common pharmacophore hypotheses (CPHs). Maximal common substructure (MCS)-based alignment method was adopted to guide the alignment of carbon molecules, deciphered the MCS atom connectivity to cluster molecules in bins and subsequently, calculated the pharmacophore similarity matrix with the bin-specific reference molecules. After alignment, the carbon molecules were enriched with original atoms in their respective positions and conventional pharmacophore features were perceived. Distance-based pharmacophoric descriptors were enumerated by computing the interdistance between perceived features and MCS-aligned 'centroid' position. The descriptor set and biological activities were used to develop support vector machine models to predict the activities of the external test set. Finally, fitness score was estimated based on pharmacophore similarity with its bin-specific reference molecules to recognize the best and poor alignments and, also with each reference molecule to predict outliers of the quantitative hypothesis model. We applied this procedure to a diverse data-set of 40 HIV-1 integrase inhibitors and discussed its effectiveness with the reported CPH model. PMID:24735019

  7. Quantitative, real-time analysis of base excision repair activity in cell lysates utilizing lesion-specific molecular beacons.

    PubMed

    Svilar, David; Vens, Conchita; Sobol, Robert W

    2012-01-01

    We describe a method for the quantitative, real-time measurement of DNA glycosylase and AP endonuclease activities in cell nuclear lysates using base excision repair (BER) molecular beacons. The substrate (beacon) is comprised of a deoxyoligonucleotide containing a single base lesion with a 6-Carboxyfluorescein (6-FAM) moiety conjugated to the 5'end and a Dabcyl moiety conjugated to the 3' end of the oligonucleotide. The BER molecular beacon is 43 bases in length and the sequence is designed to promote the formation of a stem-loop structure with 13 nucleotides in the loop and 15 base pairs in the stem. When folded in this configuration the 6-FAM moiety is quenched by Dabcyl in a non-fluorescent manner via Förster Resonance Energy Transfer (FRET). The lesion is positioned such that following base lesion removal and strand scission the remaining 5 base oligonucleotide containing the 6-FAM moiety is released from the stem. Release and detachment from the quencher (Dabcyl) results in an increase of fluorescence that is proportionate to the level of DNA repair. By collecting multiple reads of the fluorescence values, real-time assessment of BER activity is possible. The use of standard quantitative real-time PCR instruments allows the simultaneous analysis of numerous samples. The design of these BER molecular beacons, with a single base lesion, is amenable to kinetic analyses, BER quantification and inhibitor validation and is adaptable for quantification of DNA Repair activity in tissue and tumor cell lysates or with purified proteins. The analysis of BER activity in tumor lysates or tissue aspirates using these molecular beacons may be applicable to functional biomarker measurements. Further, the analysis of BER activity with purified proteins using this quantitative assay provides a rapid, high-throughput method for the discovery and validation of BER inhibitors. PMID:22895410

  8. Surface-Enhanced Raman Scattering Active Plasmonic Nanoparticles with Ultrasmall Interior Nanogap for Multiplex Quantitative Detection and Cancer Cell Imaging.

    PubMed

    Li, Jiuxing; Zhu, Zhi; Zhu, Bingqing; Ma, Yanli; Lin, Bingqian; Liu, Rudi; Song, Yanling; Lin, Hui; Tu, Song; Yang, Chaoyong

    2016-08-01

    Due to its large enhancement effect, nanostructure-based surface-enhanced Raman scattering (SERS) technology had been widely applied for bioanalysis and cell imaging. However, most SERS nanostructures suffer from poor signal reproducibility, which hinders the application of SERS nanostructures in quantitative detection. We report an etching-assisted approach to synthesize SERS-active plasmonic nanoparticles with 1 nm interior nanogap for multiplex quantitative detection and cancer cell imaging. Raman dyes and methoxy poly(ethylene glycol) thiol (mPEG-SH) were attached to gold nanoparticles (AuNPs) to prepare gold cores. Next, Ag atoms were deposited on gold cores in the presence of Pluronic F127 to form a Ag shell. HAuCl4 was used to etch the Ag shell and form an interior nanogap in Au@AgAuNPs, leading to increased Raman intensity of dyes. SERS intensity distribution of Au@AgAuNPs was found to be more uniform than that of aggregated AuNPs. Finally, Au@AgAuNPs were used for multiplex quantitative detection and cancer cell imaging. With the advantages of simple and rapid preparation of Au@AgAuNPs with highly uniform, stable, and reproducible Raman intensity, the method reported here will widen the applications of SERS-active nanoparticles in diagnostics and imaging. PMID:27385563

  9. Quantitative assessment of future development of cooper/silver resources in the Kootenai National Forest, Idaho/Montana: Part I-Estimation of the copper and silver endowments

    USGS Publications Warehouse

    Spanski, G.T.

    1992-01-01

    Faced with an ever-increasing diversity of demand for the use of public lands, managers and planners are turning more often to a multiple-use approach to meet those demands. This approach requires the uses to be mutually compatible and to utilize the more valuable attributes or resource values of the land. Therefore, it is imperative that planners be provided with all available information on attribute and resource values in a timely fashion and in a format that facilitates a comparative evaluation. The Kootenai National Forest administration enlisted the U.S. Geological Survey and U.S. Bureau of Mines to perform a quantitative assessment of future copper/silver production potential within the forest from sediment-hosted copper deposits in the Revett Formation that are similar to those being mined at the Troy Mine near Spar Lake. The U.S. Geological Survey employed a quantitative assessment technique that compared the favorable host terrane in the Kootenai area with worldwide examples of known sediment-hosted copper deposits. The assessment produced probabilistic estimates of the number of undiscovered deposits that may be present in the area and of the copper and silver endowment that might be contained in them. Results of the assessment suggest that the copper/silver deposit potential is highest in the southwestern one-third of the forest. In this area there is an estimated 50 percent probability of at least 50 additional deposits occurring mostly within approximately 260,000 acres where the Revett Formation is thought to be present in the subsurface at depths of less than 1,500 meters. A Monte Carlo type simulation using data on the grade and tonnage characteristics of other known silver-rich, sediment-hosted copper deposits predicts a 50 percent probability that these undiscovered deposits will contain at least 19 million tonnes of copper and 100,000 tonnes of silver. Combined with endowments estimated for identified, but not thoroughly explored deposits, and

  10. Effects of Stimulus Type and Strategy on Mental Rotation Network: An Activation Likelihood Estimation Meta-Analysis

    PubMed Central

    Tomasino, Barbara; Gremese, Michele

    2016-01-01

    We can predict how an object would look like if we were to see it from different viewpoints. The brain network governing mental rotation (MR) has been studied using a variety of stimuli and tasks instructions. By using activation likelihood estimation (ALE) meta-analysis we tested whether different MR networks can be modulated by the type of stimulus (body vs. non-body parts) or by the type of tasks instructions (motor imagery-based vs. non-motor imagery-based MR instructions). Testing for the bodily and non-bodily stimulus axis revealed a bilateral sensorimotor activation for bodily-related as compared to non-bodily-related stimuli and a posterior right lateralized activation for non-bodily-related as compared to bodily-related stimuli. A top-down modulation of the network was exerted by the MR tasks instructions with a bilateral (preferentially sensorimotor left) network for motor imagery- vs. non-motor imagery-based MR instructions and the latter activating a preferentially posterior right occipito-temporal-parietal network. The present quantitative meta-analysis summarizes and amends previous descriptions of the brain network related to MR and shows how it is modulated by top-down and bottom-up experimental factors. PMID:26779003

  11. Semisynthesis and quantitative structure-activity relationship (QSAR) study of some cholesterol-based hydrazone derivatives as insecticidal agents.

    PubMed

    Yang, Chun; Shao, Yonghua; Zhi, Xiaoyan; Huan, Qu; Yu, Xiang; Yao, Xiaojun; Xu, Hui

    2013-09-01

    In continuation of our program aimed at the discovery and development of natural-product-based insecticidal agents, four series of novel cholesterol-based hydrazone derivatives were synthesized, and their insecticidal activity was tested against the pre-third-instar larvae of oriental armyworm, Mythimna separata (Walker) in vivo at 1mg/mL. All the derivatives showed the better insecticidal activity than their precursor cholesterol. Quantitative structure-activity relationship (QSAR) model demonstrated that six descriptors such as RDF085v, Mor06u, Mor11u, Dv, HATS0v and H-046, are likely to influence the insecticidal activity of these compounds. Among them, two important ones are the Mor06u and RDF085v. PMID:23891182

  12. Improving consumption rate estimates by incorporating wild activity into a bioenergetics model.

    PubMed

    Brodie, Stephanie; Taylor, Matthew D; Smith, James A; Suthers, Iain M; Gray, Charles A; Payne, Nicholas L

    2016-04-01

    Consumption is the basis of metabolic and trophic ecology and is used to assess an animal's trophic impact. The contribution of activity to an animal's energy budget is an important parameter when estimating consumption, yet activity is usually measured in captive animals. Developments in telemetry have allowed the energetic costs of activity to be measured for wild animals; however, wild activity is seldom incorporated into estimates of consumption rates. We calculated the consumption rate of a free-ranging marine predator (yellowtail kingfish, Seriola lalandi) by integrating the energetic cost of free-ranging activity into a bioenergetics model. Accelerometry transmitters were used in conjunction with laboratory respirometry trials to estimate kingfish active metabolic rate in the wild. These field-derived consumption rate estimates were compared with those estimated by two traditional bioenergetics methods. The first method derived routine swimming speed from fish morphology as an index of activity (a "morphometric" method), and the second considered activity as a fixed proportion of standard metabolic rate (a "physiological" method). The mean consumption rate for free-ranging kingfish measured by accelerometry was 152 J·g(-1)·day(-1), which lay between the estimates from the morphometric method (μ = 134 J·g(-1)·day(-1)) and the physiological method (μ = 181 J·g(-1)·day(-1)). Incorporating field-derived activity values resulted in the smallest variance in log-normally distributed consumption rates (σ = 0.31), compared with the morphometric (σ = 0.57) and physiological (σ = 0.78) methods. Incorporating field-derived activity into bioenergetics models probably provided more realistic estimates of consumption rate compared with the traditional methods, which may further our understanding of trophic interactions that underpin ecosystem-based fisheries management. The general methods used to estimate active metabolic rates of free-ranging fish

  13. Use of a monoclonal antibody specific for activated endothelial cells to quantitate angiogenesis in vivo in zebrafish after drug treatment.

    PubMed

    Seng, Wen Lin; Eng, Kurt; Lee, Jenny; McGrath, Patricia

    2004-01-01

    We have recently generated a monoclonal antibody (mAb), Phy-V002, which specifically labels activated vascular endothelial cells (EC) in zebrafish. Here, we show that this mAb labels activated EC in newly formed vessels in vivo without staining mature vessels or other tissues. Using this mAb, drug effects on in vivo EC migration and vessel formation were visually assessed by whole-mount immunochemical staining in the transparent embryo. In addition, we have developed a quantitative microplate-based ELISA that measures EC proliferation in vivo after drug treatment. We have validated the quantitative in vivo ELISA using several antiangiogenic small molecules with different mechanisms of action which were added directly to the fish water. Some of these drugs, including: 2-methoxyestradiol, flavopiridol, paclitaxel, and genistein, are currently in clinical trials. We also injected large molecule drugs, including 3TSR and TSR2+KRFK, recombinant human antiangiogenic peptides of thrombospondin-1, a natural protein. To demonstrate that proangiogenic effects can also be assessed in zebrafish, we assessed effects of penicillamine and simvastatin, two proangiogenic compounds shown to stimulate vessel formation in rodents. Using whole-mount immunochemical staining with Phy-V002, inhibition of EC migration and inhibition or stimulation of vessel formation were visually observed for each compound. Next, using the quantitative in vivo angiogenesis ELISA, we generated dose-response curves for each compound. Compared to conventional assays, advantages of using zebrafish to assess drug effects on angiogenesis include: (1) a short assay time; (2) easy animal maintenance; (3) use of small quantities of drug; (4) single dosing; (5) a quantitative assay format; and (6) use of statistically significant number of animals per test. PMID:15609079

  14. Brain electromagnetic activity and lightning: potentially congruent scale-invariant quantitative properties

    PubMed Central

    Persinger, Michael A.

    2012-01-01

    The space-time characteristics of the axonal action potential are remarkably similar to the scaled equivalents of lightning. The energy and current densities from these transients within their respective volumes or cross-sectional areas are the same order of magnitude. Length–velocity ratios and temporal durations are nearly identical. There are similar chemical consequences such as the production of nitric oxide. Careful, quantitative examination of the characteristics of lightning may reveal analogous features of the action potential that could lead to a more accurate understanding of these powerful correlates of neurocognitive processes. PMID:22615688

  15. Active/passive microwave sensor comparison of MIZ-ice concentration estimates. [Marginal Ice Zone (MIZ)

    NASA Technical Reports Server (NTRS)

    Burns, B. A.; Cavalieri, D. J.; Keller, M. R.

    1986-01-01

    Active and passive microwave data collected during the 1984 summer Marginal Ice Zone Experiment in the Fram Strait (MIZEX 84) are used to compare ice concentration estimates derived from synthetic aperture radar (SAR) data to those obtained from passive microwave imagery at several frequencies. The comparison is carried out to evaluate SAR performance against the more established passive microwave technique, and to investigate discrepancies in terms of how ice surface conditions, imaging geometry, and choice of algorithm parameters affect each sensor. Active and passive estimates of ice concentration agree on average to within 12%. Estimates from the multichannel passive microwave data show best agreement with the SAR estimates because the multichannel algorithm effectively accounts for the range in ice floe brightness temperatures observed in the MIZ.

  16. Development of quantitative structure-activity relationship (QSAR) models to predict the carcinogenic potency of chemicals

    SciTech Connect

    Venkatapathy, Raghuraman Wang Chingyi; Bruce, Robert Mark; Moudgal, Chandrika

    2009-01-15

    Determining the carcinogenicity and carcinogenic potency of new chemicals is both a labor-intensive and time-consuming process. In order to expedite the screening process, there is a need to identify alternative toxicity measures that may be used as surrogates for carcinogenic potency. Alternative toxicity measures for carcinogenic potency currently being used in the literature include lethal dose (dose that kills 50% of a study population [LD{sub 50}]), lowest-observed-adverse-effect-level (LOAEL) and maximum tolerated dose (MTD). The purpose of this study was to investigate the correlation between tumor dose (TD{sub 50}) and three alternative toxicity measures as an estimator of carcinogenic potency. A second aim of this study was to develop a Classification and Regression Tree (CART) between TD{sub 50} and estimated/experimental predictor variables to predict the carcinogenic potency of new chemicals. Rat TD{sub 50}s of 590 structurally diverse chemicals were obtained from the Cancer Potency Database, and the three alternative toxicity measures considered in this study were estimated using TOPKAT, a toxicity estimation software. Though poor correlations were obtained between carcinogenic potency and the three alternative toxicity (both experimental and TOPKAT) measures for the CPDB chemicals, a CART developed using experimental data with no missing values as predictor variables provided reasonable estimates of TD{sub 50} for nine chemicals that were part of an external validation set. However, if experimental values for the three alternative measures, mutagenicity and logP are not available in the literature, then either the CART developed using missing experimental values or estimated values may be used for making a prediction.

  17. Quantitative structure-activation barrier relationship modeling for Diels-Alder ligations utilizing quantum chemical structural descriptors

    PubMed Central

    2013-01-01

    Background In the present study, we show the correlation of quantum chemical structural descriptors with the activation barriers of the Diels-Alder ligations. A set of 72 non-catalysed Diels-Alder reactions were subjected to quantitative structure-activation barrier relationship (QSABR) under the framework of theoretical quantum chemical descriptors calculated solely from the structures of diene and dienophile reactants. Experimental activation barrier data were obtained from literature. Descriptors were computed using Hartree-Fock theory using 6-31G(d) basis set as implemented in Gaussian 09 software. Results Variable selection and model development were carried out by stepwise multiple linear regression methodology. Predictive performance of the quantitative structure-activation barrier relationship (QSABR) model was assessed by training and test set concept and by calculating leave-one-out cross-validated Q2 and predictive R2 values. The QSABR model can explain and predict 86.5% and 80% of the variances, respectively, in the activation energy barrier training data. Alternatively, a neural network model based on back propagation of errors was developed to assess the nonlinearity of the sought correlations between theoretical descriptors and experimental reaction barriers. Conclusions A reasonable predictability for the activation barrier of the test set reactions was obtained, which enabled an exploration and interpretation of the significant variables responsible for Diels-Alder interaction between dienes and dienophiles. Thus, studies in the direction of QSABR modelling that provide efficient and fast prediction of activation barriers of the Diels-Alder reactions turn out to be a meaningful alternative to transition state theory based computation. PMID:24171724

  18. Non-exercise estimation of VO2max using the International Physical Activity Questionnaire

    PubMed Central

    Schembre, Susan M.; Riebe, Deborah A.

    2011-01-01

    Non-exercise equations developed from self-reported physical activity can estimate maximal oxygen uptake (VO2max) as well as submaximal exercise testing. The International Physical Activity Questionnaire (IPAQ) is the most widely used and validated self-report measure of physical activity. This study aimed to develop and test a VO2max estimation equation derived from the IPAQ-Short Form (IPAQ-S). College-aged males and females (n = 80) completed the IPAQ-S and performed a maximal exercise test. The estimation equation was created with multivariate regression in a gender-balanced subsample of participants, equally representing five levels of fitness (n = 50) and validated in the remaining participants (n = 30). The resulting equation explained 43% of the variance in measured VO2max (SEE = 5.45 ml·kg-1·min-1). Estimated VO2max for 87% of individuals fell within acceptable limits of error observed with submaximal exercise testing (20% error). The IPAQ-S can be used to successfully estimate VO2max as well as submaximal exercise tests. Development of other population-specific estimation equations is warranted. PMID:21927551

  19. Quantitative Estimation of Chemical Weathering versus Total Denudation Ratio within Tributaries of Yangtze River Basin Based on Size Dependent Chemical Composition Ratio of River Sediment

    NASA Astrophysics Data System (ADS)

    Kuboki, Y.; Chao, L.; Tada, R.; Saito, K.; Zheng, H.; Irino, T.; He, M.; Ke, W.; Suzuki, Y.

    2014-12-01

    Quantitative estimation of chemical weathering rate and evaluation of its controlling factors are critical to understand its role on landscape evolution and carbon cycle on a long time scale. In order to reconstruct the past changes in intensities of chemical weathering and erosion, it is necessary to establish a proxy for chemical versus physical weathering intensities based on chemical composition of sediments. However, the chemical composition of sediments is controlled not only by chemical weathering, but by type of source rock and grain size, too. This study aims to develop a method to quantitatively evaluate the contribution of chemical weathering relative to total denudation in the entire Yangtze River basin based on chemical composition of three different grain size fractions of river sediments. Chemical compositions of three different grain size fractions, and grain size distribution of suspended particles and river bed sediments as well as chemical composition of dissolved materials of water samples are analyzed. The result revealed that suspended particles and river bed sediments are composed of three components, aluminosilicate, quartz, and carbonate. K/Al is smaller in the smallest size fraction. We preliminary interpret that original composition of aluminosilcates within different size fractions of the same sample is the same, and the decrease in K/Al with decreasing grain size would reflect increasing influence of chemical weathering. If correct, K/Al of fine to coarse fraction can be used as an index of chemical weathering intensity. To test this idea, we examined the relationship between K/Al of fine to coarse fraction and the ratio of chemical weathering contribution to total denudation rate based on observational data. The result will be presented and its implication will be discussed.

  20. Shielding and activity estimator for template-based nuclide identification methods

    DOEpatents

    Nelson, Karl Einar

    2013-04-09

    According to one embodiment, a method for estimating an activity of one or more radio-nuclides includes receiving one or more templates, the one or more templates corresponding to one or more radio-nuclides which contribute to a probable solution, receiving one or more weighting factors, each weighting factor representing a contribution of one radio-nuclide to the probable solution, computing an effective areal density for each of the one more radio-nuclides, computing an effective atomic number (Z) for each of the one more radio-nuclides, computing an effective metric for each of the one or more radio-nuclides, and computing an estimated activity for each of the one or more radio-nuclides. In other embodiments, computer program products, systems, and other methods are presented for estimating an activity of one or more radio-nuclides.

  1. Personalizing energy expenditure estimation using physiological signals normalization during activities of daily living.

    PubMed

    Altini, Marco; Penders, Julien; Vullers, Ruud; Amft, Oliver

    2014-09-01

    In this paper we propose a generic approach to reduce inter-individual variability of different physiological signals (HR, GSR and respiration) by automatically estimating normalization parameters (e.g. baseline and range). The proposed normalization procedure does not require a dedicated personal calibration during system setup. On the other hand, normalization parameters are estimated at system runtime from sedentary and low intensity activities of daily living (ADLs), such as lying and walking. When combined with activity-specific energy expenditure (EE) models, our normalization procedure improved EE estimation by 15 to 33% in a study group of 18 participants, compared to state of the art activity-specific EE models combining accelerometer and non-normalized physiological signals. PMID:25120177

  2. Synthesis, biological evaluation, mechanism of action and quantitative structure-activity relationship studies of chalcones as antibacterial agents.

    PubMed</