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Sample records for activity quantitative estimates

  1. Principles of Quantitative Estimation of the Chaperone-Like Activity

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Molecular chaperones are able to interact with unfolded states of the protein molecule preventing their aggregation and facilitating folding of the polypeptide chain into the native structure. An understanding of the mechanism of protein aggregation is required to estimate the efficiency of action of chaperones in the test-systems based on the suppression of aggregation of protein substrates. The kinetic regimes of aggregation of proteins are discussed. The analysis of the aggregation kinetics of proteins shows that after passing the lag phase, aggregation follows, as a rule, first order kinetics. The quantitative characterization methods of the ability of chaperones to prevent aggregation of protein substrates have been elaborated.

  2. Quantitative estimation of activity and quality for collections of functional genetic elements.

    Science.gov (United States)

    Mutalik, Vivek K; Guimaraes, Joao C; Cambray, Guillaume; Mai, Quynh-Anh; Christoffersen, Marc Juul; Martin, Lance; Yu, Ayumi; Lam, Colin; Rodriguez, Cesar; Bennett, Gaymon; Keasling, Jay D; Endy, Drew; Arkin, Adam P

    2013-04-01

    The practice of engineering biology now depends on the ad hoc reuse of genetic elements whose precise activities vary across changing contexts. Methods are lacking for researchers to affordably coordinate the quantification and analysis of part performance across varied environments, as needed to identify, evaluate and improve problematic part types. We developed an easy-to-use analysis of variance (ANOVA) framework for quantifying the performance of genetic elements. For proof of concept, we assembled and analyzed combinations of prokaryotic transcription and translation initiation elements in Escherichia coli. We determined how estimation of part activity relates to the number of unique element combinations tested, and we show how to estimate expected ensemble-wide part activity from just one or two measurements. We propose a new statistic, biomolecular part 'quality', for tracking quantitative variation in part performance across changing contexts.

  3. CORAL: quantitative structure-activity relationship models for estimating toxicity of organic compounds in rats.

    Science.gov (United States)

    Toropova, A P; Toropov, A A; Benfenati, E; Gini, G; Leszczynska, D; Leszczynski, J

    2011-09-01

    For six random splits, one-variable models of rat toxicity (minus decimal logarithm of the 50% lethal dose [pLD50], oral exposure) have been calculated with CORAL software (http://www.insilico.eu/coral/). The total number of considered compounds is 689. New additional global attributes of the simplified molecular input line entry system (SMILES) have been examined for improvement of the optimal SMILES-based descriptors. These global SMILES attributes are representing the presence of some chemical elements and different kinds of chemical bonds (double, triple, and stereochemical). The "classic" scheme of building up quantitative structure-property/activity relationships and the balance of correlations (BC) with the ideal slopes were compared. For all six random splits, best prediction takes place if the aforementioned BC along with the global SMILES attributes are included in the modeling process. The average statistical characteristics for the external test set are the following: n = 119 ± 6.4, R(2) = 0.7371 ± 0.013, and root mean square error = 0.360 ± 0.037. Copyright © 2011 Wiley Periodicals, Inc.

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

    Science.gov (United States)

    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.

  5. A Comparison of Three Quantitative Methods to Estimate G6PD Activity in the Chittagong Hill Tracts, Bangladesh

    Science.gov (United States)

    Ley, Benedikt; Alam, Mohammad Shafiul; O’Donnell, James J.; Hossain, Mohammad Sharif; Kibria, Mohammad Golam; Jahan, Nusrat; Khan, Wasif A.; Thriemer, Kamala; Chatfield, Mark D.; Price, Ric N.; Richards, Jack S.

    2017-01-01

    Background Glucose-6-phosphate-dehydrogenase-deficiency (G6PDd) is a major risk factor for primaquine-induced haemolysis. There is a need for improved point-of-care and laboratory-based G6PD diagnostics to unsure safe use of primaquine. Methods G6PD activities of participants in a cross-sectional survey in Bangladesh were assessed using two novel quantitative assays, the modified WST-8 test and the CareStart™ G6PD Biosensor (Access Bio), The results were compared with a gold standard UV spectrophotometry assay (Randox). The handheld CareStart™ Hb instrument (Access Bio) is designed to be a companion instrument to the CareStart™ G6PD biosensor, and its performance was compared to the well-validated HemoCue™ method. All quantitative G6PD results were normalized with the HemoCue™ result. Results A total of 1002 individuals were enrolled. The adjusted male median (AMM) derived by spectrophotometry was 7.03 U/g Hb (interquartile range (IQR): 5.38–8.69), by WST-8 was 7.03 U/g Hb (IQR: 5.22–8.16) and by Biosensor was 8.61 U/g Hb (IQR: 6.71–10.08). The AMM between spectrophotometry and WST-8 did not differ (p = 1.0) but differed significantly between spectrophotometry and Biosensor (p0.05). Sensitivity and specificity for detecting G6PD activity <30% was 0.55 (95% confidence interval (95%CI): 0.44–0.66) and 0.98 (95%CI: 0.97–0.99) respectively for the WST-8 and 0.19 (95%CI: 0.12–0.29) and 0.99 (95%CI: 0.98–0.99) respectively for the Biosensor. Hb concentrations measured by HemoCue™ and CareStart™ Hb were strongly correlated (rs = 0.8, p<0.001, mean difference = 0.09 g Hb/dL, 95% LoA: -2.15 to 2.34). Conclusion WST-8 and the CareStart™ G6PD Biosensor represent advances in G6PD diagnostics in resource poor settings, but will require further development before clinical deployment. The CareStart™ Hb instrument produced a precise measure of haemoglobin concentration. PMID:28121993

  6. River Forecasting Center Quantitative Precipitation Estimate Archive

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — Radar indicated-rain gage verified and corrected hourly precipitation estimate on a corrected ~4km HRAP grid. This archive contains hourly estimates of precipitation...

  7. Femoral head activity in Perthes' disease: clinical evaluation of a quantitative technique for estimating tracer uptake. [/sup 99m/Tc-polyphosphate or diphosphenate

    Energy Technology Data Exchange (ETDEWEB)

    Morley, T.R.; Short, M.D.; Dowsett, D.J.

    1978-08-01

    A method for quantifying the uptake of Tc-99m-labeled phosphate complexes in the femoral head has been clinically evaluated, being used specifically for studying the uptake of these bone-seeking agents in Perthes's disease. The analysis depends on the selection, by computer program, of a reliable reference area in the femoral shaft, which is then compared with the mean uptake from each femoral head. The femoral-head activity is then represented as an uptake ratio. These ratios, together with a fixed contour representing the uptake in the femoral-head regions, provide more clinical information than the radiograph or scintiphoto, particularly in the early stages of unilateral or bilateral femoral-head disease and during followup. No correlation has been found between these ratios and qualitative techniques for assessing Perthes' disease by radiograph. From the quantitative data so far obtained it is clear that osteotomy reduces the vascularity of the femoral head, and in certain cases this reduction persists for some years. Tc-99m-labeled diphosphonate compounds were used in more recent studies, and a significant increase in sensitivity was obtained, compared with earlier polyphosphate data.

  8. Quantitative study of single molecule location estimation techniques.

    Science.gov (United States)

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

    2009-12-21

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

  9. Bayesian parameter estimation in spectral quantitative photoacoustic tomography

    Science.gov (United States)

    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.

  10. Quantitative Phytochemical Estimation and Evaluation of Hepatoprotective Activity of Methanolic Extract of Dendrobium ovatum (L. Kraenzl. Whole Plant against CCl4 Induced Hepatotoxicity

    Directory of Open Access Journals (Sweden)

    Seru Ganapaty

    2013-09-01

    Full Text Available A large number of populations suffer due to various reasons from hepatic diseases of unknown origin. The development of antihepatotoxic drugs being a major thrust area has drawn the attention of workers in the field of natural product research because synthetic drugs may cause serious side effects. The present research was aimed to study the in vivo hepatoprotective activity of methanolic extract of Dendrobium ovatum (L. Kraenzl. Whole plant, which was used traditionally in Chittoor and Khammam districts of Andhra Pradesh, by carbon tetrachloride (CCl4 induced hepatotoxicity animal model and standard drug silymarin. The level of serum aspartate aminotransferase (SGOT, alanine aminotransferase (SGPT, alkaline phosphatase (ALP and total bilirubin (T. BILI. were determined to assay hepatotoxicity. CCl4 administration caused severe hepatic damage in rats as evidenced by elevated serum SGOT, SGPT, ALP and T. BILI. Levels. The D. ovatum and silymarin administration prevented the toxic effect of CCl4 on the above serum parameters in both preventive and curative models. The present study concludes that, methanolic extract of D. ovatum has significant hepatoprotective activity against CCl4 induced hepatotoxicity, which support folkloric utilization and further confirmed by the histological investigation. The observed activity may be associated with its high bioactive compounds including flavonoids, alkaloids, triterpenoids, glycosides, steroids and carbohydrates.

  11. Quantitative Estimation of Transmitted and Reflected Lamb Waves at Discontinuity

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Hyung Jin; Sohn, Hoon [Korea Advanced Institute of Science and Technology, Daejeon (Korea, Republic of)

    2010-08-15

    For the application of Lamb wave to structural health monitoring(SHM), understanding its physical characteristic and interaction between Lamb wave and defect of the host structure is an important issue. In this study, reflected, transmitted and mode converted Lamb waves at discontinuity of a plate structure were simulated and the amplitude ratios are calculated theoretically using Modal decomposition method. The predicted results were verified comparing with finite element method(FEM) and experimental results simulating attached PZTs. The result shows that the theoretical prediction is close to the FEM and the experimental verification. Moreover, quantitative estimation method was suggested using amplitude ratio of Lamb wave at discontinuity

  12. Quantitative estimation of Nipah virus replication kinetics in vitro

    Directory of Open Access Journals (Sweden)

    Hassan Sharifah

    2006-06-01

    Full Text Available Abstract Background Nipah virus is a zoonotic virus isolated from an outbreak in Malaysia in 1998. The virus causes infections in humans, pigs, and several other domestic animals. It has also been isolated from fruit bats. The pathogenesis of Nipah virus infection is still not well described. In the present study, Nipah virus replication kinetics were estimated from infection of African green monkey kidney cells (Vero using the one-step SYBR® Green I-based quantitative real-time reverse transcriptase-polymerase chain reaction (qRT-PCR assay. Results The qRT-PCR had a dynamic range of at least seven orders of magnitude and can detect Nipah virus from as low as one PFU/μL. Following initiation of infection, it was estimated that Nipah virus RNA doubles at every ~40 minutes and attained peak intracellular virus RNA level of ~8.4 log PFU/μL at about 32 hours post-infection (PI. Significant extracellular Nipah virus RNA release occurred only after 8 hours PI and the level peaked at ~7.9 log PFU/μL at 64 hours PI. The estimated rate of Nipah virus RNA released into the cell culture medium was ~0.07 log PFU/μL per hour and less than 10% of the released Nipah virus RNA was infectious. Conclusion The SYBR® Green I-based qRT-PCR assay enabled quantitative assessment of Nipah virus RNA synthesis in Vero cells. A low rate of Nipah virus extracellular RNA release and low infectious virus yield together with extensive syncytial formation during the infection support a cell-to-cell spread mechanism for Nipah virus infection.

  13. Handling uncertainty in quantitative estimates in integrated resource planning

    Energy Technology Data Exchange (ETDEWEB)

    Tonn, B.E. [Oak Ridge National Lab., TN (United States); Wagner, C.G. [Univ. of Tennessee, Knoxville, TN (United States). Dept. of Mathematics

    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

    Science.gov (United States)

    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. Radar-Derived Quantitative Precipitation Estimation Based on Precipitation Classification

    Directory of Open Access Journals (Sweden)

    Lili Yang

    2016-01-01

    Full Text Available A method for improving radar-derived quantitative precipitation estimation is proposed. Tropical vertical profiles of reflectivity (VPRs are first determined from multiple VPRs. Upon identifying a tropical VPR, the event can be further classified as either tropical-stratiform or tropical-convective rainfall by a fuzzy logic (FL algorithm. Based on the precipitation-type fields, the reflectivity values are converted into rainfall rate using a Z-R relationship. In order to evaluate the performance of this rainfall classification scheme, three experiments were conducted using three months of data and two study cases. In Experiment I, the Weather Surveillance Radar-1988 Doppler (WSR-88D default Z-R relationship was applied. In Experiment II, the precipitation regime was separated into convective and stratiform rainfall using the FL algorithm, and corresponding Z-R relationships were used. In Experiment III, the precipitation regime was separated into convective, stratiform, and tropical rainfall, and the corresponding Z-R relationships were applied. The results show that the rainfall rates obtained from all three experiments match closely with the gauge observations, although Experiment II could solve the underestimation, when compared to Experiment I. Experiment III significantly reduced this underestimation and generated the most accurate radar estimates of rain rate among the three experiments.

  16. Quantitative Estimates of Bio-Remodeling on Coastal Rock Surfaces

    Directory of Open Access Journals (Sweden)

    Marta Pappalardo

    2016-05-01

    Full Text Available Remodeling of rocky coasts and erosion rates have been widely studied in past years, but not all the involved processes acting over rocks surface have been quantitatively evaluated yet. The first goal of this paper is to revise the different methodologies employed in the quantification of the effect of biotic agents on rocks exposed to coastal morphologic agents, comparing their efficiency. Secondly, we focus on geological methods to assess and quantify bio-remodeling, presenting some case studies in an area of the Mediterranean Sea in which different geological methods, inspired from the revised literature, have been tested in order to provide a quantitative assessment of the effects some biological covers exert over rocky platforms in tidal and supra-tidal environments. In particular, different experimental designs based on Schmidt hammer test results have been applied in order to estimate rock hardness related to different orders of littoral platforms and the bio-erosive/bio-protective role of Chthamalus ssp. and Verrucariaadriatica. All data collected have been analyzed using statistical tests to evaluate the significance of the measures and methodologies. The effectiveness of this approach is analyzed, and its limits are highlighted. In order to overcome the latter, a strategy combining geological and experimental–computational approaches is proposed, potentially capable of revealing novel clues on bio-erosion dynamics. An experimental-computational proposal, to assess the indirect effects of the biofilm coverage of rocky shores, is presented in this paper, focusing on the shear forces exerted during hydration-dehydration cycles. The results of computational modeling can be compared to experimental evidence, from nanoscopic to macroscopic scales.

  17. Quantitative Model for Estimating Soil Erosion Rates Using 137Cs

    Institute of Scientific and Technical Information of China (English)

    YANGHAO; GHANGQING; 等

    1998-01-01

    A quantitative model was developed to relate the amount of 137Cs loss from the soil profile to the rate of soil erosion,According th mass balance model,the depth distribution pattern of 137Cs in the soil profile ,the radioactive decay of 137Cs,sampling year and the difference of 137Cs fallout amount among years were taken into consideration.By introducing typical depth distribution functions of 137Cs into the model ,detailed equations for the model were got for different soil,The model shows that the rate of soil erosion is mainly controlled by the depth distrbution pattern of 137Cs ,the year of sampling,and the percentage reduction in total 137Cs,The relationship between the rate of soil loss and 137Cs depletion i neither linear nor logarithmic,The depth distribution pattern of 137Cs is a major factor for estimating the rate of soil loss,Soil erosion rate is directly related with the fraction of 137Cs content near the soil surface. The influences of the radioactive decay of 137Cs,sampling year and 137Cs input fraction are not large compared with others.

  18. Novel whole brain segmentation and volume estimation using quantitative MRI

    Energy Technology Data Exchange (ETDEWEB)

    West, J. [Linkoeping University, Radiation Physics, Department of Medical and Health Sciences, Faculty of Health Sciences, Linkoeping (Sweden); Linkoeping University, Center for Medical Imaging Science and Visualization (CMIV), Linkoeping (Sweden); SyntheticMR AB, Linkoeping (Sweden); Warntjes, J.B.M. [Linkoeping University, Center for Medical Imaging Science and Visualization (CMIV), Linkoeping (Sweden); SyntheticMR AB, Linkoeping (Sweden); Linkoeping University and Department of Clinical Physiology UHL, County Council of Oestergoetland, Clinical Physiology, Department of Medical and Health Sciences, Faculty of Health Sciences, Linkoeping (Sweden); Lundberg, P. [Linkoeping University, Center for Medical Imaging Science and Visualization (CMIV), Linkoeping (Sweden); Linkoeping University and Department of Radiation Physics UHL, County Council of Oestergoetland, Radiation Physics, Department of Medical and Health Sciences, Faculty of Health Sciences, Linkoeping (Sweden); Linkoeping University and Department of Radiology UHL, County Council of Oestergoetland, Radiology, Department of Medical and Health Sciences, Faculty of Health Sciences, Linkoeping (Sweden)

    2012-05-15

    Brain segmentation and volume estimation of grey matter (GM), white matter (WM) and cerebro-spinal fluid (CSF) are important for many neurological applications. Volumetric changes are observed in multiple sclerosis (MS), Alzheimer's disease and dementia, and in normal aging. A novel method is presented to segment brain tissue based on quantitative magnetic resonance imaging (qMRI) of the longitudinal relaxation rate R{sub 1}, the transverse relaxation rate R{sub 2} and the proton density, PD. Previously reported qMRI values for WM, GM and CSF were used to define tissues and a Bloch simulation performed to investigate R{sub 1}, R{sub 2} and PD for tissue mixtures in the presence of noise. Based on the simulations a lookup grid was constructed to relate tissue partial volume to the R{sub 1}-R{sub 2}-PD space. The method was validated in 10 healthy subjects. MRI data were acquired using six resolutions and three geometries. Repeatability for different resolutions was 3.2% for WM, 3.2% for GM, 1.0% for CSF and 2.2% for total brain volume. Repeatability for different geometries was 8.5% for WM, 9.4% for GM, 2.4% for CSF and 2.4% for total brain volume. We propose a new robust qMRI-based approach which we demonstrate in a patient with MS. (orig.)

  19. Quantitative estimates of the volatility of ambient organic aerosol

    Directory of Open Access Journals (Sweden)

    C. D. Cappa

    2010-01-01

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

  20. Real Time River Forecasting Center Quantitative Precipitation Estimate

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — Radar indicated-rain gage verified and corrected hourly precipitation estimate on a corrected ~4km HRAP grid. This archive contains hourly estimates of precipitation...

  1. Quantitative CT: technique dependence of volume estimation on pulmonary nodules.

    Science.gov (United States)

    Chen, Baiyu; Barnhart, Huiman; Richard, Samuel; Colsher, James; Amurao, Maxwell; Samei, Ehsan

    2012-03-07

    Current estimation of lung nodule size typically relies on uni- or bi-dimensional techniques. While new three-dimensional volume estimation techniques using MDCT have improved size estimation of nodules with irregular shapes, the effect of acquisition and reconstruction parameters on accuracy (bias) and precision (variance) of the new techniques has not been fully investigated. To characterize the volume estimation performance dependence on these parameters, an anthropomorphic chest phantom containing synthetic nodules was scanned and reconstructed with protocols across various acquisition and reconstruction parameters. Nodule volumes were estimated by a clinical lung analysis software package, LungVCAR. Precision and accuracy of the volume assessment were calculated across the nodules and compared between protocols via a generalized estimating equation analysis. Results showed that the precision and accuracy of nodule volume quantifications were dependent on slice thickness, with different dependences for different nodule characteristics. Other parameters including kVp, pitch, and reconstruction kernel had lower impact. Determining these technique dependences enables better volume quantification via protocol optimization and highlights the importance of consistent imaging parameters in sequential examinations.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

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

    2010-08-01

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

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  6. nowCOAST's Map Service for NOAA Quantitative Precipitation Estimates (Time Enabled)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Map Information: This nowCOAST time-enabled map service provides maps depicting the NWS Multi-Radar Multi-Sensor (MRMS) quantitative precipitation estimate mosaics...

  7. A Quantitative Model to Estimate Drug Resistance in Pathogens

    Directory of Open Access Journals (Sweden)

    Frazier N. Baker

    2016-12-01

    Full Text Available Pneumocystis pneumonia (PCP is an opportunistic infection that occurs in humans and other mammals with debilitated immune systems. These infections are caused by fungi in the genus Pneumocystis, which are not susceptible to standard antifungal agents. Despite decades of research and drug development, the primary treatment and prophylaxis for PCP remains a combination of trimethoprim (TMP and sulfamethoxazole (SMX that targets two enzymes in folic acid biosynthesis, dihydrofolate reductase (DHFR and dihydropteroate synthase (DHPS, respectively. There is growing evidence of emerging resistance by Pneumocystis jirovecii (the species that infects humans to TMP-SMX associated with mutations in the targeted enzymes. In the present study, we report the development of an accurate quantitative model to predict changes in the binding affinity of inhibitors (Ki, IC50 to the mutated proteins. The model is based on evolutionary information and amino acid covariance analysis. Predicted changes in binding affinity upon mutations highly correlate with the experimentally measured data. While trained on Pneumocystis jirovecii DHFR/TMP data, the model shows similar or better performance when evaluated on the resistance data for a different inhibitor of PjDFHR, another drug/target pair (PjDHPS/SMX and another organism (Staphylococcus aureus DHFR/TMP. Therefore, we anticipate that the developed prediction model will be useful in the evaluation of possible resistance of the newly sequenced variants of the pathogen and can be extended to other drug targets and organisms.

  8. Quantitative Method of Measuring Metastatic Activity

    Science.gov (United States)

    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.

  9. Estimation of effects of quantitative trait loci in large complex pedigrees

    NARCIS (Netherlands)

    Meuwissen, T.H.E.; Goddard, M.E.

    1997-01-01

    A method was derived to estimate effects of quantitative trait loci (QTL) using incomplete genotype information in large outbreeding populations with complex pedigrees. The method accounts for background genes by estimating polygenic effects. The basic equations used are very similar to the usual li

  10. Vertical activity estimation using 2D radar

    CSIR Research Space (South Africa)

    Hakl, H

    2008-12-01

    Full Text Available airspace control response. The method for qualitative vertical activity estimation as presented is characterised by a very fast response time and requires minimal sensor input. The method relies on the interplay of two opposing motion prediction models...

  11. Quantitative estimates of the surface habitability of Kepler-452b

    Science.gov (United States)

    Silva, Laura; Vladilo, Giovanni; Murante, Giuseppe; Provenzale, Antonello

    2017-09-01

    Kepler-452b is currently the best example of an Earth-size planet in the habitable zone of a sun-like star, a type of planet whose number of detections is expected to increase in the future. Searching for biosignatures in the supposedly thin atmospheres of these planets is a challenging goal that requires a careful selection of the targets. Under the assumption of a rocky-dominated nature for Kepler-452b, we considered it as a test case to calculate a temperature-dependent habitability index, h050, designed to maximize the potential presence of biosignature-producing activity. The surface temperature has been computed for a broad range of climate factors using a climate model designed for terrestrial-type exoplanets. After fixing the planetary data according to the experimental results, we changed the surface gravity, CO2 abundance, surface pressure, orbital eccentricity, rotation period, axis obliquity and ocean fraction within the range of validity of our model. For most choices of parameters, we find habitable solutions with h050 > 0.2 only for CO2 partial pressure p_CO_2 ≲ 0.04 bar. At this limiting value of CO2 abundance, the planet is still habitable if the total pressure is p ≲ 2 bar. In all cases, the habitability drops for eccentricity e ≳ 0.3. Changes of rotation period and obliquity affect the habitability through their impact on the equator-pole temperature difference rather than on the mean global temperature. We calculated the variation of h050 resulting from the luminosity evolution of the host star for a wide range of input parameters. Only a small combination of parameters yields habitability-weighted lifetimes ≳2 Gyr, sufficiently long to develop atmospheric biosignatures still detectable at the present time.

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

    OpenAIRE

    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-ac...

  13. Quantitative Analysis of VIIRS DNB Nightlight Point Source for Light Power Estimation and Stability Monitoring

    Directory of Open Access Journals (Sweden)

    Changyong Cao

    2014-12-01

    Full Text Available The high sensitivity and advanced onboard calibration on the Visible Infrared Imaging Radiometer Suite (VIIRS Day/Night Band (DNB enables accurate measurements of low light radiances which leads to enhanced quantitative applications at night. The finer spatial resolution of DNB also allows users to examine social economic activities at urban scales. Given the growing interest in the use of the DNB data, there is a pressing need for better understanding of the calibration stability and absolute accuracy of the DNB at low radiances. The low light calibration accuracy was previously estimated at a moderate 15% using extended sources while the long-term stability has yet to be characterized. There are also several science related questions to be answered, for example, how the Earth’s atmosphere and surface variability contribute to the stability of the DNB measured radiances; how to separate them from instrument calibration stability; whether or not SI (International System of Units traceable active light sources can be designed and installed at selected sites to monitor the calibration stability, radiometric and geolocation accuracy, and point spread functions of the DNB; furthermore, whether or not such active light sources can be used for detecting environmental changes, such as aerosols. This paper explores the quantitative analysis of nightlight point sources, such as those from fishing vessels, bridges, and cities, using fundamental radiometry and radiative transfer, which would be useful for a number of applications including search and rescue in severe weather events, as well as calibration/validation of the DNB. Time series of the bridge light data are used to assess the stability of the light measurements and the calibration of VIIRS DNB. It was found that the light radiant power computed from the VIIRS DNB data matched relatively well with independent assessments based on the in situ light installations, although estimates have to be

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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…

  17. Estimating an Activity Driven Hidden Markov Model

    OpenAIRE

    Meyer, David A.; Shakeel, Asif

    2015-01-01

    We define a Hidden Markov Model (HMM) in which each hidden state has time-dependent $\\textit{activity levels}$ that drive transitions and emissions, and show how to estimate its parameters. Our construction is motivated by the problem of inferring human mobility on sub-daily time scales from, for example, mobile phone records.

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

    Science.gov (United States)

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

    2015-03-01

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

  19. Software Size Estimation Using Activity Point

    Science.gov (United States)

    Densumite, S.; Muenchaisri, P.

    2017-03-01

    Software size is widely recognized as an important parameter for effort and cost estimation. Currently there are many methods for measuring software size including Source Line of Code (SLOC), Function Points (FP), Netherlands Software Metrics Users Association (NESMA), Common Software Measurement International Consortium (COSMIC), and Use Case Points (UCP). SLOC is physically counted after the software is developed. Other methods compute size from functional, technical, and/or environment aspects at early phase of software development. In this research, activity point approach is proposed to be another software size estimation method. Activity point is computed using activity diagram and adjusted with technical complexity factors (TCF), environment complexity factors (ECF), and people risk factors (PRF). An evaluation of the approach is present.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  1. A new TLC bioautographic assay for qualitative and quantitative estimation of lipase inhibitors.

    Science.gov (United States)

    Tang, Jihe; Zhou, Jinge; Tang, Qingjiu; Wu, Tao; Cheng, Zhihong

    2016-01-01

    Lipase inhibitory assays based on TLC bioautography have made recent progress; however, an assay with greater substrate specificity and quantitative capabilities would advance the efficacy of this particular bioassay. To address these limitations, a new TLC bioautographic assay for detecting lipase inhibitors was developed and validated in this study. The new TLC bioautographic assay was based on reaction of lipase with β-naphthyl myristate and the subsequent formation of the purple dye between β-naphthol and Fast Blue B salt (FBB). The relative lipase inhibitory capacity (RLIC) was determined by a TLC densitometry with fluorescence detection, expressed as orlistat equivalents in millimoles on a per sample weight basis. Six pure compounds and three natural extracts were evaluated for their potential lipase inhibitory activities by this TLC bioautographic assay. The β-naphthyl myristate as the substrate improved the detection sensitivity and specificity significantly. The limit of detection (LOD) of this assay was 0.01 ng for orlistat, the current treatment for obesity. This assay has acceptable accuracy (92.07-105.39%), intra-day and inter-day precisions [relative standard deviation (RSD), 2.64-4.40%], as well as intra-plate and inter-plate precisions (RSD, 1.8-4.9%). The developed method is rapid, simple, stable, and specific for screening and estimation of the potential lipase inhibitors. Copyright © 2015 John Wiley & Sons, Ltd.

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

    Science.gov (United States)

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

    2014-07-01

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

  3. ESTIMATION OF COMPETITIVE ACTIVITY IN SYNCHRONIZED SWIMMING

    Directory of Open Access Journals (Sweden)

    Shul'ga L.M.

    2013-01-01

    Full Text Available Aim – is to develop the approach to technical complexity estimation of free routine composition in synchronized swimming. Were analyzed and considered free routine compositions of the strongest swimmers in European and World Championships during the period under study (2008-2011. In the research took part 32 qualified athletes different ages. Were determined the options of the constructed of free program and location the combination saturation in those programs. Were established complicated elements distribution by the minutes of the free routine composition performance and developed the approach to technical complexity estimation of free routine composition (solo for using in training and competitive activity for qualified athletes in synchronized swimming. The total time of breath-holding makes up 40% of the time of the whole free routine composition.

  4. Parameter Estimation in Active Plate Structures

    DEFF Research Database (Denmark)

    Araujo, A. L.; Lopes, H. M. R.; Vaz, M. A. P.

    2006-01-01

    In this paper two non-destructive methods for elastic and piezoelectric parameter estimation in active plate structures with surface bonded piezoelectric patches are presented. These methods rely on experimental undamped natural frequencies of free vibration. The first solves the inverse problem...... through gradient based optimization techniques, while the second is based on a metamodel of the inverse problem, using artificial neural networks. A numerical higher order finite element laminated plate model is used in both methods and results are compared and discussed through a simulated...

  5. Improvement and quantitative performance estimation of the back support muscle suit.

    Science.gov (United States)

    Muramatsu, Y; Umehara, H; Kobayashi, H

    2013-01-01

    We have been developing the wearable muscle suit for direct and physical motion supports. The use of the McKibben artificial muscle has opened the way to the introduction of "muscle suits" compact, lightweight, reliable, wearable "assist-bots" enabling manual worker to lift and carry weights. Since back pain is the most serious problem for manual worker, improvement of the back support muscle suit under the feasibility study and quantitative estimation are shown in this paper. The structure of the upper body frame, the method to attach to the body, and the axes addition were explained as for the improvement. In the experiments, we investigated quantitative performance results and efficiency of the back support muscle suit in terms of vertical lifting of heavy weights by employing integral electromyography (IEMG). The results indicated that the values of IEMG were reduced by about 40% by using the muscle suit.

  6. Direct Estimation of Optical Parameters From Photoacoustic Time Series in Quantitative Photoacoustic Tomography.

    Science.gov (United States)

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

    2016-11-01

    Estimation of optical absorption and scattering of a target is an inverse problem associated with quantitative photoacoustic tomography. Conventionally, the problem is expressed as two folded. First, images of initial pressure distribution created by absorption of a light pulse are formed based on acoustic boundary measurements. Then, the optical properties are determined based on these photoacoustic images. The optical stage of the inverse problem can thus suffer from, for example, artefacts caused by the acoustic stage. These could be caused by imperfections in the acoustic measurement setting, of which an example is a limited view acoustic measurement geometry. In this work, the forward model of quantitative photoacoustic tomography is treated as a coupled acoustic and optical model and the inverse problem is solved by using a Bayesian approach. Spatial distribution of the optical properties of the imaged target are estimated directly from the photoacoustic time series in varying acoustic detection and optical illumination configurations. It is numerically demonstrated, that estimation of optical properties of the imaged target is feasible in limited view acoustic detection setting.

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

    Science.gov (United States)

    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.

  8. Detection and parameter estimation for quantitative trait loci using regression models and multiple markers

    Directory of Open Access Journals (Sweden)

    Schook Lawrence B

    2000-07-01

    Full Text Available Abstract A strategy of multi-step minimal conditional regression analysis has been developed to determine the existence of statistical testing and parameter estimation for a quantitative trait locus (QTL that are unaffected by linked QTLs. The estimation of marker-QTL recombination frequency needs to consider only three cases: 1 the chromosome has only one QTL, 2 one side of the target QTL has one or more QTLs, and 3 either side of the target QTL has one or more QTLs. Analytical formula was derived to estimate marker-QTL recombination frequency for each of the three cases. The formula involves two flanking markers for case 1, two flanking markers plus a conditional marker for case 2, and two flanking markers plus two conditional markers for case 3. Each QTL variance and effect, and the total QTL variance were also estimated using analytical formulae. Simulation data show that the formulae for estimating marker-QTL recombination frequency could be a useful statistical tool for fine QTL mapping. With 1 000 observations, a QTL could be mapped to a narrow chromosome region of 1.5 cM if no linked QTL is present, and to a 2.8 cM chromosome region if either side of the target QTL has at least one linked QTL.

  9. Novel Sessile Drop Software for Quantitative Estimation of Slag Foaming in Carbon/Slag Interactions

    Science.gov (United States)

    Khanna, Rita; Rahman, Mahfuzur; Leow, Richard; Sahajwalla, Veena

    2007-08-01

    Novel video-processing software has been developed for the sessile drop technique for a rapid and quantitative estimation of slag foaming. The data processing was carried out in two stages: the first stage involved the initial transformation of digital video/audio signals into a format compatible with computing software, and the second stage involved the computation of slag droplet volume and area of contact in a chosen video frame. Experimental results are presented on slag foaming from synthetic graphite/slag system at 1550 °C. This technique can be used for determining the extent and stability of foam as a function of time.

  10. Diagnosis and quantitative estimation of pulmonary congestion or edema by pulmonary CT numbers

    Energy Technology Data Exchange (ETDEWEB)

    Kato, Shiro; Nakamoto, Takaaki

    1987-12-01

    Pulmonary computed tomography (CT) was performed in 25 patients with left heart failure and 10 healthy persons to diagnose pulmonary congestion or edema associated with left heart failure. In an analysis of histogram for pulmonary CT numbers obtained from CT scans, CT numbers indicating pulmonary edema were defined as -650 to -750 H.U. This allowed pulmonary edema to be quantitatively estimated early when abnormal findings were not available on chest X-ray film or pulmonary circulation studies. Histograms for CT numbers could be displayed by colors on CT scans. (Namekawa, K.).

  11. RESERCH CONCERNING THE ESTIMATE OF QUANTITATIVE AND QUALITATIVE PHYSIOLOGICAL GROUP BACTERIA IN PEATS SAMPLE

    Directory of Open Access Journals (Sweden)

    ADRIANA CRISTE

    2013-12-01

    Full Text Available The total aerobe micro flora can be determined on solid mediums for the aerobe bacteria and this relive quantity of micro organisms from the peat samples. The quantitative evaluation was done using solid nutritive mediums which allows the estimation of nr CFU/g as well observing the morphology of the colonies and their utility through their emplacement and morphological and biochemical characterization of isolated strains.. The evaluations where done through the method of dilution, using selective liquid mediums. Every day the characteristic reaction of the respective group was observed, either through the metabolising of the substrate, or through the appearance of a catabolic product in the medium.

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

    Science.gov (United States)

    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.

  13. An Integrated Method of Multiradar Quantitative Precipitation Estimation Based on Cloud Classification and Dynamic Error Analysis

    Directory of Open Access Journals (Sweden)

    Yong Huang

    2017-01-01

    Full Text Available Relationships between radar reflectivity factor and rainfall are different in various precipitation cloud systems. In this study, the cloud systems are firstly classified into five categories with radar and satellite data to improve radar quantitative precipitation estimation (QPE algorithm. Secondly, the errors of multiradar QPE algorithms are assumed to be different in convective and stratiform clouds. The QPE data are then derived with methods of Z-R, Kalman filter (KF, optimum interpolation (OI, Kalman filter plus optimum interpolation (KFOI, and average calibration (AC based on error analysis on the Huaihe River Basin. In the case of flood on the early of July 2007, the KFOI is applied to obtain the QPE product. Applications show that the KFOI can improve precision of estimating precipitation for multiple precipitation types.

  14. Estimation of genetic parameters and detection of quantitative trait loci for metabolites in Danish Holstein milk

    DEFF Research Database (Denmark)

    Buitenhuis, Albert Johannes; Sundekilde, Ulrik; Poulsen, Nina Aagaard;

    2013-01-01

    Small components and metabolites in milk are significant for the utilization of milk, not only in dairy food production but also as disease predictors in dairy cattle. This study focused on estimation of genetic parameters and detection of quantitative trait loci for metabolites in bovine milk....... For this purpose, milk samples were collected in mid lactation from 371 Danish Holstein cows in first to third parity. A total of 31 metabolites were detected and identified in bovine milk by using 1H nuclear magnetic resonance (NMR) spectroscopy. Cows were genotyped using a bovine high-density single nucleotide...... polymorphism (SNP) chip. Based on the SNP data, a genomic relationship matrix was calculated and used as a random factor in a model together with 2 fixed factors (herd and lactation stage) to estimate the heritability and breeding value for individual metabolites in the milk. Heritability was in the range of 0...

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  16. Estimation of financial loss ratio for E-insurance:a quantitative model

    Institute of Scientific and Technical Information of China (English)

    钟元生; 陈德人; 施敏华

    2002-01-01

    In view of the risk of E-commerce and the response of the insurance industry to it, this paper is aimed at one important point of insurance, that is, estimation of financial loss ratio, which is one of the most difficult problems facing the E-insurance industry. This paper proposes a quantitative analyzing model for estimating E-insurance financial loss ratio. The model is based on gross income per enterprise and CSI/FBI computer crime and security survey. The analysis results presented are reasonable and valuable for both insurer and the insured and thus can be accepted by both of them. What we must point out is that according to our assumption, the financial loss ratio varied very little, 0.233% in 1999 and 0.236% in 2000 although there was much variation in the main data of the CSI/FBI survey.

  17. Estimation of qualitative and quantitative characteristics interrelation, having an impact on amount of tourists in hospitality industry

    Directory of Open Access Journals (Sweden)

    Tatyana P. Levchenko

    2011-01-01

    Full Text Available The article considers methods of estimation of qualitative and quantitative characteristics interrelation, having impact on amount of tourists in hospitality industry, offers the latest technologies of the given indicators calculation.

  18. A hierarchical statistical model for estimating population properties of quantitative genes

    Directory of Open Access Journals (Sweden)

    Wu Rongling

    2002-06-01

    Full Text Available Abstract Background Earlier methods for detecting major genes responsible for a quantitative trait rely critically upon a well-structured pedigree in which the segregation pattern of genes exactly follow Mendelian inheritance laws. However, for many outcrossing species, such pedigrees are not available and genes also display population properties. Results In this paper, a hierarchical statistical model is proposed to monitor the existence of a major gene based on its segregation and transmission across two successive generations. The model is implemented with an EM algorithm to provide maximum likelihood estimates for genetic parameters of the major locus. This new method is successfully applied to identify an additive gene having a large effect on stem height growth of aspen trees. The estimates of population genetic parameters for this major gene can be generalized to the original breeding population from which the parents were sampled. A simulation study is presented to evaluate finite sample properties of the model. Conclusions A hierarchical model was derived for detecting major genes affecting a quantitative trait based on progeny tests of outcrossing species. The new model takes into account the population genetic properties of genes and is expected to enhance the accuracy, precision and power of gene detection.

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

    Science.gov (United States)

    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.

  20. Sleep Period Time Estimation Based on Electrodermal Activity.

    Science.gov (United States)

    Hwang, Su Hwan; Seo, Sangwon; Yoon, Hee Nam; Jung, Da Woon; Baek, Hyun Jae; Cho, Jaegeol; Choi, Jae Won; Lee, Yu Jin; Jeong, Do-Un; Park, Kwang Suk

    2017-01-01

    We proposed and tested a method to estimate sleep period time (SPT) using electrodermal activity (EDA) signals. Eight healthy subjects and six obstructive sleep apnea patients participated in the experiments. Each subject's EDA signals were measured at the middle and ring fingers of the dominant hand during polysomnography (PSG). For nine of the 17 participants, wrist actigraphy was also measured for a quantitative comparison of EDA- and actigraphy-based methods. Based on the training data, we observed that sleep onset was accompanied by a gradual reduction of amplitude of the EDA signals, whereas sleep offset was accompanied by a rapid increase in amplitude of EDA signals. We developed a method based on these EDA fluctuations during sleep-wake transitions, and applied it to a test dataset. The performance of the method was assessed by comparing its results with those from a physician's sleep stage scores. The mean absolute errors in the obtained values for sleep onset, offset, and period time between the proposed method, and the results of the PSG were 4.1, 3.0, and 6.1 min, respectively. Furthermore, there were no significant differences in the corresponding values between the methods. We compared these results with those obtained by applying actigraphic methods, and found that our algorithm outperformed these in terms of each estimated parameter of interest in SPT estimation. Long awakening periods were also detected based on sympathetic responses reflected in the EDA signals. The proposed method can be applied to a daily sleep monitoring system.

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

    Energy Technology Data Exchange (ETDEWEB)

    Waters, M.D. [Environmental Protection Agency, Washington, DC (United States); Stack, H.F.; Garrett, N.E.; Jackson, M.A. [Environmental Health Research and Testing, Inc., Research Triangle Park, NC (United States)

    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.

  2. Quantitative analysis of wrist electrodermal activity during sleep

    OpenAIRE

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

    2014-01-01

    We present the first quantitative characterization of electrodermal activity (EDA) patterns on the wrists of healthy adults during sleep using dry electrodes. We compare the new results on the wrist to 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 hea...

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

    Science.gov (United States)

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

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

  4. Quantitative Retention-Activity Relationship Studies by Liposome Electrokinetic Chromatography to Predict Skin Permeability

    Institute of Scientific and Technical Information of China (English)

    XIAN De-Ling; HUANG Ke-Long; LIU Su-Qin; XIAO Jing-Yi

    2008-01-01

    Liposome electrokinetic chromatography (LEKC) provides a simple and facile approach for drug membrane interactions using liposome as a pseudostationary phase. This study evaluated the potential of LEKC for high-throughput skin permeability profiled as an in vitro technique. A quantitative retention-activity relationship(QRAR) model for the estimation of skin permeability was proposed. For the 16 structurally diverse chemicals, lg k correlated well with permeability values (R2=0.886). The predictive ability of the model was evaluated by cross-validation. The result was compared to traditional quantitative structure-activity relationship, QSAR, models using some molecular descriptors and physicochemical parameters. Interestingly, a single LEKC retention parameter was capable of describing the skin permeability, while three variables in QSAR were needed to achieve a similar correlation (R2=0.704). The QRAR models developed in this paper may be a useful method to screening new chemicals and in the early stage of development and selection of chemicals.

  5. A quantitative approach for comparing modeled biospheric carbon flux estimates across regional scales

    Directory of Open Access Journals (Sweden)

    D. N. Huntzinger

    2010-10-01

    Full Text Available Given the large differences between biospheric model estimates of regional carbon exchange, there is a need to understand and reconcile the predicted spatial variability of fluxes across models. This paper presents a set of quantitative tools that can be applied for comparing flux estimates in light of the inherent differences in model formulation. The presented methods include variogram analysis, variable selection, and geostatistical regression. These methods are evaluated in terms of their ability to assess and identify differences in spatial variability in flux estimates across North America among a small subset of models, as well as differences in the environmental drivers that appear to have the greatest control over the spatial variability of predicted fluxes. The examined models are the Simple Biosphere (SiB 3.0, Carnegie Ames Stanford Approach (CASA, and CASA coupled with the Global Fire Emissions Database (CASA GFEDv2, and the analyses are performed on model-predicted net ecosystem exchange, gross primary production, and ecosystem respiration. Variogram analysis reveals consistent seasonal differences in spatial variability among modeled fluxes at a 1°×1° spatial resolution. However, significant differences are observed in the overall magnitude of the carbon flux spatial variability across models, in both net ecosystem exchange and component fluxes. Results of the variable selection and geostatistical regression analyses suggest fundamental differences between the models in terms of the factors that control the spatial variability of predicted flux. For example, carbon flux is more strongly correlated with percent land cover in CASA GFEDv2 than in SiB or CASA. Some of these factors can be linked back to model formulation, and would have been difficult to identify simply by comparing net fluxes between models. Overall, the quantitative approach presented here provides a set of tools for comparing predicted grid-scale fluxes across

  6. Application of short-wave infrared (SWIR) spectroscopy in quantitative estimation of clay mineral contents

    Science.gov (United States)

    You, Jinfeng; Xing, Lixin; Liang, Liheng; Pan, Jun; Meng, Tao

    2014-03-01

    Clay minerals are significant constituents of soil which are necessary for life. This paper studied three types of clay minerals, kaolinite, illite, and montmorillonite, for they are not only the most common soil forming materials, but also important indicators of soil expansion and shrinkage potential. These clay minerals showed diagnostic absorption bands resulting from vibrations of hydroxyl groups and structural water molecules in the SWIR wavelength region. The short-wave infrared reflectance spectra of the soil was obtained from a Portable Near Infrared Spectrometer (PNIS, spectrum range: 1300~2500 nm, interval: 2 nm). Due to the simplicity, quickness, and the non-destructiveness analysis, SWIR spectroscopy has been widely used in geological prospecting, chemical engineering and many other fields. The aim of this study was to use multiple linear regression (MLR) and partial least squares (PLS) regression to establish the optimizing quantitative estimation models of the kaolinite, illite and montmorillonite contents from soil reflectance spectra. Here, the soil reflectance spectra mainly refers to the spectral reflectivity of soil (SRS) corresponding to the absorption-band position (AP) of kaolinite, illite, and montmorillonite representative spectra from USGS spectral library, the SRS corresponding to the AP of soil spectral and soil overall spectrum reflectance values. The optimal estimation models of three kinds of clay mineral contents showed that the retrieval accuracy was satisfactory (Kaolinite content: a Root Mean Square Error of Calibration (RMSEC) of 1.671 with a coefficient of determination (R2) of 0.791; Illite content: a RMSEC of 1.126 with a R2 of 0.616; Montmorillonite content: a RMSEC of 1.814 with a R2 of 0.707). Thus, the reflectance spectra of soil obtained form PNIS could be used for quantitative estimation of kaolinite, illite and montmorillonite contents in soil.

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

    Science.gov (United States)

    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

  8. Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits.

    Science.gov (United States)

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

    2013-05-01

    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.

  9. Estimating the number of integrations in transformed plants by quantitative real-time PCR

    Directory of Open Access Journals (Sweden)

    Vaira Anna Maria

    2002-10-01

    Full Text Available Abstract Background When generating transformed plants, a first step in their characterization is to obtain, for each new line, an estimate of how many copies of the transgene have been integrated in the plant genome because this can deeply influence the level of transgene expression and the ease of stabilizing expression in following generations. This task is normally achieved by Southern analysis, a procedure that requires relatively large amounts of plant material and is both costly and labour-intensive. Moreover, in the presence of rearranged copies the estimates are not correct. New approaches to the problem could be of great help for plant biotechnologists. Results By using a quantitative real-time PCR method that requires limited preliminary optimisation steps, we achieved statistically significant estimates of 1, 2 and 3 copies of a transgene in the primary transformants. Furthermore, by estimating the copy number of both the gene of interest and the selectable marker gene, we show that rearrangements of the T-DNA are not the exception, and probably happen more often than usually recognised. Conclusions We have developed a rapid and reliable method to estimate the number of integrated copies following genetic transformation. Unlike other similar procedures, this method is not dependent on identical amplification efficiency between the PCR systems used and does not need preliminary information on a calibrator. Its flexibility makes it appropriate in those situations where an accurate optimisation of all reaction components is impossible or impractical. Finally, the quality of the information produced is higher than what can be obtained by Southern blot analysis.

  10. Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits.

    Directory of Open Access Journals (Sweden)

    Noah Zaitlen

    2013-05-01

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  12. An Ensemble Generator for Quantitative Precipitation Estimation Based on Censored Shifted Gamma Distributions

    Science.gov (United States)

    Wright, D.; Kirschbaum, D.; Yatheendradas, S.

    2016-12-01

    The considerable uncertainties associated with quantitative precipitation estimates (QPE), whether from satellite platforms, ground-based weather radar, or numerical weather models, suggest that such QPE should be expressed as distributions or ensembles of possible values, rather than as single values. In this research, we borrow a framework from the weather forecast verification community, to "correct" satellite precipitation and generate ensemble QPE. This approach is based on the censored shifted gamma distribution (CSGD). The probability of precipitation, central tendency (i.e. mean), and the uncertainty can be captured by the three parameters of the CSGD. The CSGD can then be applied for simulation of rainfall ensembles using a flexible nonlinear regression framework, whereby the CSGD parameters can be conditioned on one or more reference rainfall datasets and on other time-varying covariates such as modeled or measured estimates of precipitable water and relative humidity. We present the framework and initial results by generating precipitation ensembles based on the Tropical Rainfall Measuring Mission Multi-satellite Precipitation Analysis (TMPA) dataset, using both NLDAS and PERSIANN-CDR precipitation datasets as references. We also incorporate a number of covariates from MERRA2 reanalysis including model-estimated precipitation, precipitable water, relative humidity, and lifting condensation level. We explore the prospects for applying the framework and other ensemble error models globally, including in regions where high-quality "ground truth" rainfall estimates are lacking. We compare the ensemble outputs against those of an independent rain gage-based ensemble rainfall dataset. "Pooling" of regional rainfall observations is explored as one option for improving ensemble estimates of rainfall extremes. The approach has potential applications in near-realtime, retrospective, and scenario modeling of rainfall-driven hazards such as floods and landslides

  13. SPECTRAL FEATURE ANALYSIS FOR QUANTITATIVE ESTIMATION OF CYANOBACTERIA CHLOROPHYLL-A

    Directory of Open Access Journals (Sweden)

    Y. Lin

    2016-06-01

    Full Text Available 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

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    Blodgett, David L.

    2013-01-01

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

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

    Science.gov (United States)

    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

  19. Quantitative analysis of axonal fiber activation evoked by deep brain stimulation via activation density heat maps

    Directory of Open Access Journals (Sweden)

    Christian J. Hartmann

    2015-02-01

    Full Text Available Background: Cortical modulation is likely to be involved in the various therapeutic effects of deep brain stimulation (DBS. However, it is currently difficult to predict the changes of cortical modulation during clinical adjustment of DBS. Therefore, we present a novel quantitative approach to estimate anatomical regions of DBS-evoked cortical modulation. Methods: Four different models of the subthalamic nucleus (STN DBS were created to represent variable electrode placements (model I: dorsal border of the posterolateral STN; model II: central posterolateral STN; model III: central anteromedial STN; model IV: dorsal border of the anteromedial STN. Axonal fibers of passage near each electrode location were reconstructed using probabilistic tractography and modeled using multi-compartment cable models. Stimulation-evoked activation of local axon fibers and corresponding cortical projections were modeled and quantified. Results: Stimulation at the border of the STN (models I and IV led to a higher degree of fiber activation and associated cortical modulation than stimulation deeply inside the STN (models II and III. A posterolateral target (models I and II was highly connected to cortical areas representing motor function. Additionally, model I was also associated with strong activation of fibers projecting to the cerebellum. Finally, models III and IV showed a dorsoventral difference of preferentially targeted prefrontal areas (models III: middle frontal gyrus; model IV: inferior frontal gyrus.Discussion: The method described herein allows characterization of cortical modulation across different electrode placements and stimulation parameters. Furthermore, knowledge of anatomical distribution of stimulation-evoked activation targeting cortical regions may help predict efficacy and potential side effects, and therefore can be used to improve the therapeutic effectiveness of individual adjustments in DBS patients.

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

    Science.gov (United States)

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

    1991-06-01

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

  1. A novel HPTLC method for quantitative estimation of biomarkers in polyherbal formulation

    Institute of Scientific and Technical Information of China (English)

    Zeeshan Ahmed Sheikh; Sadia Shakeel; Somia Gul; Aqib Zahoor; Saleha Suleman Khan; Faisal Haider Zaidi; Khan Usmanghani

    2015-01-01

    Objective:To explore the quantitative estimation of biomarkers gallic acid and berberine in polyherbal formulation Entoban syrup. Methods: High performance thin layer chromatography was performed to evaluate the presence of gallic acid and berberine employing toluene:ethyl acetate:formic acid:methanol 12:9:4:0.5 (v/v/v/v) and ethanol: water: formic acid 90:9:1 (v/v/v), as a mobile phase respectively. Results:The Rf values (0.58) for gallic acid and (0.76) for berberine in both sample and reference standard were found comparable under UV light at 273 nm and 366 nm respectively. The high performance thin layer chromatography method developed for quantization was simple, accurate and specific. Conclusions: The present standardization provides specific and accurate tool to develop qualifications for identity, transparency and reproducibility of biomarkers in Entoban syrup.

  2. A novel HPTLC method for quantitative estimation of biomarkers in polyherbal formulation

    Institute of Scientific and Technical Information of China (English)

    Zeeshan; Ahmed; Sheikh; Sadia; Shakeel; Somia; Gul; Aqib; Zahoor; Saleha; Suleman; Khan; Faisal; Haider; Zaidi; Khan; Usmanghani

    2015-01-01

    Objective: To explore the quantitative estimation of biomarkers gallic acid and berberine in polyherbal formulation Entoban syrup.Methods: High performance thin layer chromatography was performed to evaluate the presence of gallic acid and berberine employing toluene: ethyl acetate: formic acid:methanol 12:9:4:0.5(v/v/v/v) and ethanol: water: formic acid 90:9:1(v/v/v), as a mobile phase respectively.Results: The R f values(0.58) for gallic acid and(0.76) for berberine in both sample and reference standard were found comparable under UV light at 273 nm and 366 nm respectively. The high performance thin layer chromatography method developed for quantization was simple, accurate and specific.Conclusions: The present standardization provides specific and accurate tool to develop qualifications for identity, transparency and reproducibility of biomarkers in Entoban syrup.

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

    Science.gov (United States)

    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.

  4. Parameter estimation using the genetic algorithm and its impact on quantitative precipitation forecast

    Directory of Open Access Journals (Sweden)

    Y. H. Lee

    2006-12-01

    Full Text Available In this study, optimal parameter estimations are performed for both physical and computational parameters in a mesoscale meteorological model, and their impacts on the quantitative precipitation forecasting (QPF are assessed for a heavy rainfall case occurred at the Korean Peninsula in June 2005. Experiments are carried out using the PSU/NCAR MM5 model and the genetic algorithm (GA for two parameters: the reduction rate of the convective available potential energy in the Kain-Fritsch (KF scheme for cumulus parameterization, and the Asselin filter parameter for numerical stability. The fitness function is defined based on a QPF skill score. It turns out that each optimized parameter significantly improves the QPF skill. Such improvement is maximized when the two optimized parameters are used simultaneously. Our results indicate that optimizations of computational parameters as well as physical parameters and their adequate applications are essential in improving model performance.

  5. Method for quantitative estimation of position perception using a joystick during linear movement.

    Science.gov (United States)

    Wada, Y; Tanaka, M; Mori, S; Chen, Y; Sumigama, S; Naito, H; Maeda, M; Yamamoto, M; Watanabe, S; Kajitani, N

    1996-12-01

    We designed a method for quantitatively estimating self-motion perceptions during passive body movement on a sled. The subjects were instructed to tilt a joystick in proportion to perceived displacement from a giving starting position during linear movement with varying displacements of 4 m, 10 m and 16 m induced by constant acceleration of 0.02 g, 0.05 g and 0.08 g along the antero-posterior axis. With this method, we could monitor not only subjective position perceptions but also response latencies for the beginning (RLbgn) and end (RLend) of the linear movement. Perceived body position fitted Stevens' power law, where R=kSn (R is output of the joystick, k is a constant, S is the displacement from the linear movement and n is an exponent). RLbgn decreased as linear acceleration increased. We conclude that this method is useful in analyzing the features and sensitivities of self-motion perceptions during movement.

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

    Science.gov (United States)

    Vives, Sergi; Salicrú, Miquel

    2005-05-01

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

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

    Science.gov (United States)

    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.

  8. Fatalities in high altitude mountaineering: a review of quantitative risk estimates.

    Science.gov (United States)

    Weinbruch, Stephan; Nordby, Karl-Christian

    2013-12-01

    Quantitative estimates for mortality in high altitude mountaineering are reviewed. Special emphasis is placed on the heterogeneity of the risk estimates and on confounding. Crude estimates for mortality are on the order of 1/1000 to 40/1000 persons above base camp, for both expedition members and high altitude porters. High altitude porters have mostly a lower risk than expedition members (risk ratio for all Nepalese peaks requiring an expedition permit: 0.73; 95 % confidence interval 0.59-0.89). The summit bid is generally the most dangerous part of an expedition for members, whereas most high altitude porters die during route preparation. On 8000 m peaks, the mortality during descent from summit varies between 4/1000 and 134/1000 summiteers (members plus porters). The risk estimates are confounded by human and environmental factors. Information on confounding by gender and age is contradictory and requires further work. There are indications for safety segregation of men and women, with women being more risk averse than men. Citizenship appears to be a significant confounder. Prior high altitude mountaineering experience in Nepal has no protective effect. Commercial expeditions in the Nepalese Himalayas have a lower mortality than traditional expeditions, though after controlling for confounding, the difference is not statistically significant. The overall mortality is increasing with increasing peak altitude for expedition members but not for high altitude porters. In the Nepalese Himalayas and in Alaska, a significant decrease of mortality with calendar year was observed. A few suggestions for further work are made at the end of the article.

  9. Comparison of Quantitative Structure-Activity Relationship Model Performances on Carboquinone Derivatives

    Directory of Open Access Journals (Sweden)

    Sorana D. Bolboaca

    2009-01-01

    Full Text Available Quantitative structure-activity relationship (qSAR models are used to understand how the structure and activity of chemical compounds relate. In the present study, 37 carboquinone derivatives were evaluated and two different qSAR models were developed using members of the Molecular Descriptors Family (MDF and the Molecular Descriptors Family on Vertices (MDFV. The usual parameters of regression models and the following estimators were defined and calculated in order to analyze the validity and to compare the models: Akaike?s information criteria (three parameters, Schwarz (or Bayesian information criterion, Amemiya prediction criterion, Hannan-Quinn criterion, Kubinyi function, Steiger's Z test, and Akaike's weights. The MDF and MDFV models proved to have the same estimation ability of the goodness-of-fit according to Steiger's Z test. The MDFV model proved to be the best model for the considered carboquinone derivatives according to the defined information and prediction criteria, Kubinyi function, and Akaike's weights.

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

    Science.gov (United States)

    Wallace, Jack

    2010-05-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Eto, Shuzo, E-mail: eto@criepi.denken.or.jp [Central Research Institute of Electric Power Industry, 2-6-1 Nagasaka, Yokosuka, Kanagawa 240-0196 (Japan); Matsuo, Toyofumi; Matsumura, Takuro; Fujii, Takashi [Central Research Institute of Electric Power Industry, 2-6-1 Nagasaka, Yokosuka, Kanagawa 240-0196 (Japan); Tanaka, Masayoshi Y. [Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 2-6-1 Nagasaka, Yokosuka, Kanagawa 240-0196 (Japan)

    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 mm{sup 2} 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. - Highlights: • We estimated the carbonation depth and the apparent diffusion coefficient of chlorine sodium in the reinforced concrete with cracking damage by LIBS. • Two-dimensional profile measurement of the emission intensity in each element was performed to visualize the chloride penetration and the carbonation in the reinforced concrete. • Apparent diffusion coefficient of chlorine and sodium can be estimated using the Fick

  12. Quantitative control of organ shape by combinatorial gene activity.

    Directory of Open Access Journals (Sweden)

    Min-Long Cui

    Full Text Available The development of organs with particular shapes, like wings or flowers, depends on regional activity of transcription factors and signalling molecules. However, the mechanisms that link these molecular activities to the morphogenetic events underlying shape are poorly understood. Here we describe a combination of experimental and computational approaches that address this problem, applying them to a group of genes controlling flower shape in the Snapdragon (Antirrhinum. Four transcription factors are known to play a key role in the control of floral shape and asymmetry in Snapdragon. We use quantitative shape analysis of mutants for these factors to define principal components underlying flower shape variation. We show that each transcription factor has a specific effect on the shape and size of regions within the flower, shifting the position of the flower in shape space. These shifts are further analysed by generating double mutants and lines that express some of the genes ectopically. By integrating these observations with known gene expression patterns and interactions, we arrive at a combinatorial scheme for how regional effects on shape are genetically controlled. We evaluate our scheme by incorporating the proposed interactions into a generative model, where the developing flower is treated as a material sheet that grows according to how genes modify local polarities and growth rates. The petal shapes generated by the model show a good quantitative match with those observed experimentally for each petal in numerous genotypes, thus validating the hypothesised scheme. This article therefore shows how complex shapes can be accounted for by combinatorial effects of transcription factors on regional growth properties. This finding has implications not only for how shapes develop but also for how they may have evolved through tinkering with transcription factors and their targets.

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

    Science.gov (United States)

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

    2012-09-01

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

  14. Sensitivity of quantitative groundwater recharge estimates to volumetric and distribution uncertainty in rainfall forcing products

    Science.gov (United States)

    Werner, Micha; Westerhoff, Rogier; Moore, Catherine

    2017-04-01

    Quantitative estimates of recharge due to precipitation excess are an important input to determining sustainable abstraction of groundwater resources, as well providing one of the boundary conditions required for numerical groundwater modelling. Simple water balance models are widely applied for calculating recharge. In these models, precipitation is partitioned between different processes and stores; including surface runoff and infiltration, storage in the unsaturated zone, evaporation, capillary processes, and recharge to groundwater. Clearly the estimation of recharge amounts will depend on the estimation of precipitation volumes, which may vary, depending on the source of precipitation data used. However, the partitioning between the different processes is in many cases governed by (variable) intensity thresholds. This means that the estimates of recharge will not only be sensitive to input parameters such as soil type, texture, land use, potential evaporation; but mainly to the precipitation volume and intensity distribution. In this paper we explore the sensitivity of recharge estimates due to difference in precipitation volumes and intensity distribution in the rainfall forcing over the Canterbury region in New Zealand. We compare recharge rates and volumes using a simple water balance model that is forced using rainfall and evaporation data from; the NIWA Virtual Climate Station Network (VCSN) data (which is considered as the reference dataset); the ERA-Interim/WATCH dataset at 0.25 degrees and 0.5 degrees resolution; the TRMM-3B42 dataset; the CHIRPS dataset; and the recently releases MSWEP dataset. Recharge rates are calculated at a daily time step over the 14 year period from the 2000 to 2013 for the full Canterbury region, as well as at eight selected points distributed over the region. Lysimeter data with observed estimates of recharge are available at four of these points, as well as recharge estimates from the NGRM model, an independent model

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  18. Quantitative estimation of brain atrophy and function with PET and MRI two-dimensional projection images

    Energy Technology Data Exchange (ETDEWEB)

    Saito, Reiko; Uemura, Koji; Uchiyama, Akihiko [Waseda Univ., Tokyo (Japan). School of Science and Engineering; Toyama, Hinako; Ishii, Kenji; Senda, Michio

    2001-05-01

    The purpose of this paper is to estimate the extent of atrophy and the decline in brain function objectively and quantitatively. Two-dimensional (2D) projection images of three-dimensional (3D) transaxial images of positron emission tomography (PET) and magnetic resonance imaging (MRI) were made by means of the Mollweide method which keeps the area of the brain surface. A correlation image was generated between 2D projection images of MRI and cerebral blood flow (CBF) or {sup 18}F-fluorodeoxyglucose (FDG) PET images and the sulcus was extracted from the correlation image clustered by K-means method. Furthermore, the extent of atrophy was evaluated from the extracted sulcus on 2D-projection MRI and the cerebral cortical function such as blood flow or glucose metabolic rate was assessed in the cortex excluding sulcus on 2D-projection PET image, and then the relationship between the cerebral atrophy and function was evaluated. This method was applied to the two groups, the young and the aged normal subjects, and the relationship between the age and the rate of atrophy or the cerebral blood flow was investigated. This method was also applied to FDG-PET and MRI studies in the normal controls and in patients with corticobasal degeneration. The mean rate of atrophy in the aged group was found to be higher than that in the young. The mean value and the variance of the cerebral blood flow for the young are greater than those of the aged. The sulci were similarly extracted using either CBF or FDG PET images. The purposed method using 2-D projection images of MRI and PET is clinically useful for quantitative assessment of atrophic change and functional disorder of cerebral cortex. (author)

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

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

    2013-01-01

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

  1. Revised activation estimates for silicon carbide

    Energy Technology Data Exchange (ETDEWEB)

    Heinisch, H.L. [Pacific Northwest National Lab., Richland, WA (United States); 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.

  2. Estimating background-subtracted fluorescence transients in calcium imaging experiments: a quantitative approach.

    Science.gov (United States)

    Joucla, Sébastien; Franconville, Romain; Pippow, Andreas; Kloppenburg, Peter; Pouzat, Christophe

    2013-08-01

    Calcium imaging has become a routine technique in neuroscience for subcellular to network level investigations. The fast progresses in the development of new indicators and imaging techniques call for dedicated reliable analysis methods. In particular, efficient and quantitative background fluorescence subtraction routines would be beneficial to most of the calcium imaging research field. A background-subtracted fluorescence transients estimation method that does not require any independent background measurement is therefore developed. This method is based on a fluorescence model fitted to single-trial data using a classical nonlinear regression approach. The model includes an appropriate probabilistic description of the acquisition system's noise leading to accurate confidence intervals on all quantities of interest (background fluorescence, normalized background-subtracted fluorescence time course) when background fluorescence is homogeneous. An automatic procedure detecting background inhomogeneities inside the region of interest is also developed and is shown to be efficient on simulated data. The implementation and performances of the proposed method on experimental recordings from the mouse hypothalamus are presented in details. This method, which applies to both single-cell and bulk-stained tissues recordings, should help improving the statistical comparison of fluorescence calcium signals between experiments and studies.

  3. Estimating the Quantitative Demand of NOAC Antidote Doses on Stroke Units.

    Science.gov (United States)

    Pfeilschifter, Waltraud; Farahmand, Dana; Niemann, Daniela; Ikenberg, Benno; Hohmann, Carina; Abruscato, Mario; Thonke, Sven; Strzelczyk, Adam; Hedtmann, Günther; Neumann-Haefelin, Tobias; Kollmar, Rainer; Singer, Oliver C; Ferbert, Andreas; Steiner, Thorsten; Steinmetz, Helmuth; Reihs, Anke; Misselwitz, Björn; Foerch, Christian

    2016-01-01

    The first specific antidote for non-vitamin K antagonist oral anticoagulants (NOAC) has recently been approved. NOAC antidotes will allow specific treatment for 2 hitherto problematic patient groups: patients with oral anticoagulant therapy (OAT)-associated intracerebral hemorrhage (ICH) and maybe also thrombolysis candidates presenting on oral anticoagulation (OAT). We aimed to estimate the frequency of these events and hence the quantitative demand of antidote doses on a stroke unit. We extracted data of patients with acute ischemic stroke and ICH (demand for NOAC antidote doses on stroke units. Eighteen percent of ICH patients within 6 h of symptom onset or an unknown symptom onset were on OAT. Given a NOAC share at admission of 40%, about 7% of all ICH patients may qualify for NOAC reversal therapy. Thirteen percent of ischemic stroke patients admitted within 4 h presented on anticoagulation. Given the availability of an appropriate antidote, a NOAC share of 50% could lead to a 6.1% increase in thrombolysis rate. Stroke units serving populations with a comparable demographic structure should prepare to treat up to 1% of all acute ischemic stroke patients and 7% of all acute ICH patients with NOAC antidotes. These numbers may increase with the mounting prevalence of atrial fibrillation and an increasing use of NOAC. © 2016 S. Karger AG, Basel.

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

    Science.gov (United States)

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

    2016-06-22

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

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

    Science.gov (United States)

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

    2013-01-01

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

  6. The estimation of quantitative parameters of oligonucleotides immobilization on mica surface

    Science.gov (United States)

    Sharipov, T. I.; Bakhtizin, R. Z.

    2017-05-01

    Immobilization of nucleic acids on the surface of various materials is increasingly being used in research and some practical applications. Currently, the DNA chip technology is rapidly developing. The basis of the immobilization process can be both physical adsorption and chemisorption. A useful way to control the immobilization of nucleic acids on a surface is to use atomic force microscopy. It allows you to investigate the topography of the surface by its direct imaging with high resolution. Usually, to fix the DNA on the surface of mica are used cations which mediate the interaction between the mica surface and the DNA molecules. In our work we have developed a method for estimation of quantitative parameter of immobilization of oligonucleotides is their degree of aggregation depending on the fixation conditions on the surface of mica. The results on study of aggregation of oligonucleotides immobilized on mica surface will be presented. The single oligonucleotides molecules have been imaged clearly, whereas their surface areas have been calculated and calibration curve has been plotted.

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

    Science.gov (United States)

    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.

  8. Utilization of gel electrophoreses for the quantitative estimation of digestive enzyme papain

    Directory of Open Access Journals (Sweden)

    Magdy M. Muharram

    2017-03-01

    Full Text Available SDS-PAGE densitometric method for analysis of papain in pharmaceutical formulations was developed and validated for the first time. Standard and samples were mixed with SDS sample buffer and denatured at 95 °C for 5 min and the gel was run at 20 mA and 200 V for 30–40 min in SDS-PAGE buffer. Gels were stained in Coomassie blue solution and distained by 5% methanol and 10% acetic acid. Destained gels were imaged and analyzed using the ChemiDoc™ XRS+ System. Bands of papain appeared at Rf value 0.78 ± 0.03 corresponding to molecular weight 23406 Da between proteins with molecular weight 31,000 and 21,500 Da of the broad range protein standard. The generated calibration curve was used for quantitative estimation of papain in pharmaceutical formulations. The developed method was validated for precision, accuracy, specificity and robustness as described by the ICH guidelines. The proposed method gives an alternative approach for enzymes and protein analysis.

  9. An Experimental Study for Quantitative Estimation of Rebar Corrosion in Concrete Using Ground Penetrating Radar

    Directory of Open Access Journals (Sweden)

    Md Istiaque Hasan

    2016-01-01

    Full Text Available Corrosion of steel rebar in reinforced concrete is one the most important durability issues in the service life of a structure. In this paper, an investigation is conducted to find out the relationship between the amount of reinforced concrete corrosion and GPR maximum positive amplitude. Accelerated corrosion was simulated in the lab by impressing direct current into steel rebar that was submerged in a 5% salt water solution. The amount of corrosion was varied in the rebars with different levels of mass loss ranging from 0% to 45%. The corroded rebars were then placed into three different oil emulsion tanks having different dielectric properties similar to concrete. The maximum amplitudes from the corroded bars were recorded. A linear relationship between the maximum positive amplitudes and the amount of corrosion in terms of percentage loss of area was observed. It was proposed that the relationship between the GPR maximum amplitude and the amount of corrosion can be used as a basis of a NDE technique of quantitative estimation of corrosion.

  10. Review of Quantitative Structure - Activity Relationships for Acute Mammalian Toxicity

    Directory of Open Access Journals (Sweden)

    Iglika Lessigiarska

    2006-12-01

    Full Text Available This paper reviews Quantitative Structure-Activity Relationship (QSAR models for acute mammalian toxicity published in the last decade. A number of QSAR models based on cytotoxicity data from mammalian cell lines are also included because of their possible use as a surrogate system for predicting acute toxicity to mammals. On the basis of the review, the following conclusions can be made: i a relatively small number of models for in vivo toxicity are published in the literature. This is due to the nature of the endpoint - acute systemic toxicity is usually related to whole body phenomena and therefore is very complex. The complexity of the mechanisms involved leads to difficulties in the QSAR modelling; ii most QSAR models identify hydrophobicity as a parameter of high importance for the modelled toxicity. In addition, many models indicate the role of the electronic and steric effects; iii most of the literature-based models are restricted to single chemical classes. Models based on more heterogeneous data sets are those incorporated in expert systems. In general, the QSAR models for mammalian toxicity identified in this review are considered useful for investigating the mechanisms of toxicity of defined chemical classes. However, for predictive purposes in the regulatory assessment of chemicals most of the models require additional information to satisfy internationally agreed validation principles. In addition, the development of new models covering larger chemical domains would be useful for the regulatory assessment of chemicals.

  11. Predicting urban stormwater runoff with quantitative precipitation estimates from commercial microwave links

    Science.gov (United States)

    Pastorek, Jaroslav; Fencl, Martin; Stránský, David; Rieckermann, Jörg; Bareš, Vojtěch

    2017-04-01

    Reliable and representative rainfall data are crucial for urban runoff modelling. However, traditional precipitation measurement devices often fail to provide sufficient information about the spatial variability of rainfall, especially when heavy storm events (determining design of urban stormwater systems) are considered. Commercial microwave links (CMLs), typically very dense in urban areas, allow for indirect precipitation detection with desired spatial and temporal resolution. Fencl et al. (2016) recognised the high bias in quantitative precipitation estimates (QPEs) from CMLs which significantly limits their usability and, in order to reduce the bias, suggested a novel method for adjusting the QPEs to existing rain gauge networks. Studies evaluating the potential of CMLs for rainfall detection so far focused primarily on direct comparison of the QPEs from CMLs to ground observations. In contrast, this investigation evaluates the suitability of these innovative rainfall data for stormwater runoff modelling on a case study of a small ungauged (in long-term perspective) urban catchment in Prague-Letňany, Czech Republic (Fencl et al., 2016). We compare the runoff measured at the outlet from the catchment with the outputs of a rainfall-runoff model operated using (i) CML data adjusted by distant rain gauges, (ii) rainfall data from the distant gauges alone and (iii) data from a single temporary rain gauge located directly in the catchment, as it is common practice in drainage engineering. Uncertainties of the simulated runoff are analysed using the Bayesian method for uncertainty evaluation incorporating a statistical bias description as formulated by Del Giudice et al. (2013). Our results show that adjusted CML data are able to yield reliable runoff modelling results, primarily for rainfall events with convective character. Performance statistics, most significantly the timing of maximal discharge, reach better (less uncertain) values with the adjusted CML data

  12. Quantitative modeling of the ionospheric response to geomagnetic activity

    Directory of Open Access Journals (Sweden)

    T. J. Fuller-Rowell

    Full Text Available A physical model of the coupled thermosphere and ionosphere has been used to determine the accuracy of model predictions of the ionospheric response to geomagnetic activity, and assess our understanding of the physical processes. The physical model is driven by empirical descriptions of the high-latitude electric field and auroral precipitation, as measures of the strength of the magnetospheric sources of energy and momentum to the upper atmosphere. Both sources are keyed to the time-dependent TIROS/NOAA auroral power index. The output of the model is the departure of the ionospheric F region from the normal climatological mean. A 50-day interval towards the end of 1997 has been simulated with the model for two cases. The first simulation uses only the electric fields and auroral forcing from the empirical models, and the second has an additional source of random electric field variability. In both cases, output from the physical model is compared with F-region data from ionosonde stations. Quantitative model/data comparisons have been performed to move beyond the conventional "visual" scientific assessment, in order to determine the value of the predictions for operational use. For this study, the ionosphere at two ionosonde stations has been studied in depth, one each from the northern and southern mid-latitudes. The model clearly captures the seasonal dependence in the ionospheric response to geomagnetic activity at mid-latitude, reproducing the tendency for decreased ion density in the summer hemisphere and increased densities in winter. In contrast to the "visual" success of the model, the detailed quantitative comparisons, which are necessary for space weather applications, are less impressive. The accuracy, or value, of the model has been quantified by evaluating the daily standard deviation, the root-mean-square error, and the correlation coefficient between the data and model predictions. The modeled quiet-time variability, or standard

  13. Quantitative estimates of past changes in ITCZ position and cross-equatorial atmospheric heat transport

    Science.gov (United States)

    McGee, D.; Donohoe, A.; Marshall, J.; Ferreira, D.

    2012-12-01

    The mean position and seasonal migration of the Intertropical Convergence Zone (ITCZ) govern the intensity, spatial distribution and seasonality of precipitation throughout the tropics as well as the magnitude and direction of interhemispheric atmospheric heat transport (AHT). As a result of these links to global tropical precipitation and hemispheric heat budgets, paleoclimate studies have commonly sought to use reconstructions of local precipitation and surface winds to identify past shifts in the ITCZ's mean position or seasonal extent. Records indicate close ties between ITCZ position and interhemispheric surface temperature gradients in past climates, with the ITCZ shifting toward the warmer hemisphere. This shift would increase AHT into the cooler hemisphere to at least partially compensate for cooling there. Despite widespread qualitative evidence consistent with ITCZ shifts, few proxy records offer quantitative estimates of the distance of these shifts or of the associated changes in AHT. Here we present a strategy for placing quantitative limits on past changes in mean annual ITCZ position and interhemispheric AHT based on explorations of the modern seasonal cycle and models of present and past climates. We use reconstructions of tropical sea surface temperature gradients to place bounds on globally averaged ITCZ position and interhemispheric AHT during the Last Glacial Maximum, Heinrich Stadial 1, and the Mid-Holocene (6 ka). Though limited by the small number of SST records available, our results suggest that past shifts in the global mean ITCZ were small, typically less than 1 degree of latitude. Past changes in interhemispheric AHT may have been substantial, with anomalies approximately equal to the magnitude of modern interhemispheric AHT. Using constraints on the invariance of the total (ocean+atmosphere) heat transport we suggest possible bounds on fluctuations of the OHT and AMOC during Heinrich Stadial 1. We also explore ITCZ shifts in models and

  14. Quantitative assay for TALEN activity at endogenous genomic loci

    Directory of Open Access Journals (Sweden)

    Yu Hisano

    2013-02-01

    Artificially designed nucleases such as zinc-finger nucleases (ZFNs and transcription activator-like effector nucleases (TALENs can induce a targeted DNA double-strand break at the specific target genomic locus, leading to the frameshift-mediated gene disruption. However, the assays for their activity on the endogenous genomic loci remain limited. Herein, we describe a versatile modified lacZ assay to detect frameshifts in the nuclease target site. Short fragments of the genome DNA at the target or putative off-target loci were amplified from the genomic DNA of TALEN-treated or control embryos, and were inserted into the lacZα sequence for the conventional blue–white selection. The frequency of the frameshifts in the fragment can be estimated from the numbers of blue and white colonies. Insertions and/or deletions were easily determined by sequencing the plasmid DNAs recovered from the positive colonies. Our technique should offer broad application to the artificial nucleases for genome editing in various types of model organisms.

  15. Estimation of genetic parameters and their sampling variances for quantitative traits in the type 2 modified augmented design

    Institute of Scientific and Technical Information of China (English)

    Frank M. You; Qijian Song; Gaofeng Jia; Yanzhao Cheng; Scott Duguid; Helen Booker; Sylvie Cloutier

    2016-01-01

    The type 2 modified augmented design (MAD2) is an efficient unreplicated experimental design used for evaluating large numbers of lines in plant breeding and for assessing genetic variation in a population. Statistical methods and data adjustment for soil heterogeneity have been previously described for this design. In the absence of replicated test genotypes in MAD2, their total variance cannot be partitioned into genetic and error components as required to estimate heritability and genetic correlation of quantitative traits, the two conventional genetic parameters used for breeding selection. We propose a method of estimating the error variance of unreplicated genotypes that uses replicated controls, and then of estimating the genetic parameters. Using the Delta method, we also derived formulas for estimating the sampling variances of the genetic parameters. Computer simulations indicated that the proposed method for estimating genetic parameters and their sampling variances was feasible and the reliability of the estimates was positively associated with the level of heritability of the trait. A case study of estimating the genetic parameters of three quantitative traits, iodine value, oil content, and linolenic acid content, in a biparental recombinant inbred line population of flax with 243 individuals, was conducted using our statistical models. A joint analysis of data over multiple years and sites was suggested for genetic parameter estimation. A pipeline module using SAS and Perl was developed to facilitate data analysis and appended to the previously developed MAD data analysis pipeline (http://probes.pw.usda.gov/bioinformatics_ tools/MADPipeline/index.html).

  16. Estimation of genetic parameters and their sampling variances for quantitative traits in the type 2 modified augmented design

    Institute of Scientific and Technical Information of China (English)

    Frank M.You; Qijian Song; Gaofeng Jia; Yanzhao Cheng; Scott Duguid; Helen Booker; Sylvie Cloutier

    2016-01-01

    The type 2 modified augmented design(MAD2) is an efficient unreplicated experimental design used for evaluating large numbers of lines in plant breeding and for assessing genetic variation in a population. Statistical methods and data adjustment for soil heterogeneity have been previously described for this design. In the absence of replicated test genotypes in MAD2, their total variance cannot be partitioned into genetic and error components as required to estimate heritability and genetic correlation of quantitative traits, the two conventional genetic parameters used for breeding selection. We propose a method of estimating the error variance of unreplicated genotypes that uses replicated controls, and then of estimating the genetic parameters. Using the Delta method, we also derived formulas for estimating the sampling variances of the genetic parameters.Computer simulations indicated that the proposed method for estimating genetic parameters and their sampling variances was feasible and the reliability of the estimates was positively associated with the level of heritability of the trait. A case study of estimating the genetic parameters of three quantitative traits, iodine value, oil content, and linolenic acid content, in a biparental recombinant inbred line population of flax with 243 individuals, was conducted using our statistical models. A joint analysis of data over multiple years and sites was suggested for genetic parameter estimation. A pipeline module using SAS and Perl was developed to facilitate data analysis and appended to the previously developed MAD data analysis pipeline(http://probes.pw.usda.gov/bioinformatics_ tools/MADPipeline/index.html).

  17. Estimation of genetic parameters and their sampling variances for quantitative traits in the type 2 modified augmented design

    Directory of Open Access Journals (Sweden)

    Frank M. You

    2016-04-01

    Full Text Available The type 2 modified augmented design (MAD2 is an efficient unreplicated experimental design used for evaluating large numbers of lines in plant breeding and for assessing genetic variation in a population. Statistical methods and data adjustment for soil heterogeneity have been previously described for this design. In the absence of replicated test genotypes in MAD2, their total variance cannot be partitioned into genetic and error components as required to estimate heritability and genetic correlation of quantitative traits, the two conventional genetic parameters used for breeding selection. We propose a method of estimating the error variance of unreplicated genotypes that uses replicated controls, and then of estimating the genetic parameters. Using the Delta method, we also derived formulas for estimating the sampling variances of the genetic parameters. Computer simulations indicated that the proposed method for estimating genetic parameters and their sampling variances was feasible and the reliability of the estimates was positively associated with the level of heritability of the trait. A case study of estimating the genetic parameters of three quantitative traits, iodine value, oil content, and linolenic acid content, in a biparental recombinant inbred line population of flax with 243 individuals, was conducted using our statistical models. A joint analysis of data over multiple years and sites was suggested for genetic parameter estimation. A pipeline module using SAS and Perl was developed to facilitate data analysis and appended to the previously developed MAD data analysis pipeline (http://probes.pw.usda.gov/bioinformatics_ tools/MADPipeline/index.html.

  18. Quantitative analysis of wrist electrodermal activity during sleep.

    Science.gov (United States)

    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.

  19. Quantitative precipitation estimation in complex orography using quasi-vertical profiles of dual polarization radar variables

    Science.gov (United States)

    Montopoli, Mario; Roberto, Nicoletta; Adirosi, Elisa; Gorgucci, Eugenio; Baldini, Luca

    2017-04-01

    Weather radars are nowadays a unique tool to estimate quantitatively the rain precipitation near the surface. This is an important task for a plenty of applications. For example, to feed hydrological models, mitigate the impact of severe storms at the ground using radar information in modern warning tools as well as aid the validation studies of satellite-based rain products. With respect to the latter application, several ground validation studies of the Global Precipitation Mission (GPM) products have recently highlighted the importance of accurate QPE from ground-based weather radars. To date, a plenty of works analyzed the performance of various QPE algorithms making use of actual and synthetic experiments, possibly trained by measurement of particle size distributions and electromagnetic models. Most of these studies support the use of dual polarization variables not only to ensure a good level of radar data quality but also as a direct input in the rain estimation equations. Among others, one of the most important limiting factors in radar QPE accuracy is the vertical variability of particle size distribution that affects at different levels, all the radar variables acquired as well as rain rates. This is particularly impactful in mountainous areas where the altitudes of the radar sampling is likely several hundred of meters above the surface. In this work, we analyze the impact of the vertical profile variations of rain precipitation on several dual polarization radar QPE algorithms when they are tested a in complex orography scenario. So far, in weather radar studies, more emphasis has been given to the extrapolation strategies that make use of the signature of the vertical profiles in terms of radar co-polar reflectivity. This may limit the use of the radar vertical profiles when dual polarization QPE algorithms are considered because in that case all the radar variables used in the rain estimation process should be consistently extrapolated at the surface

  20. Evaluation of radar-gauge merging methods for quantitative precipitation estimates

    Directory of Open Access Journals (Sweden)

    E. Goudenhoofdt

    2008-10-01

    Full Text Available Accurate quantitative precipitation estimates are of crucial importance for hydrological studies and applications. When spatial precipitation fields are required, rain gauge measurements are often combined with weather radar observations. In this paper, we evaluate several radar-gauge merging methods with various degrees of complexity: from mean field bias correction to geostatical merging techniques. The study area is the Walloon region of Belgium, which is mostly located in the Meuse catchment. Observations from a C-band Doppler radar and a dense rain gauge network are used to retrieve daily rainfall accumulations over this area. The relative performance of the different merging methods are assessed through a comparison against daily measurements from an independent gauge network. A 3-year verification is performed using several statistical quality parameters. It appears that the geostatistical merging methods perform best with the mean absolute error decreasing by 40% with respect to the original data. A mean field bias correction still achieves a reduction of 25%. A seasonal analysis shows that the benefit of using radar observations is particularly significant during summer. The effect of the network density on the performance of the methods is also investigated. For this purpose, a simple approach to remove gauges from a network is proposed. The analysis reveals that the sensitivity is relatively high for the geostatistical methods but rather small for the simple methods. The geostatistical methods give the best results for all network densities except for a very low density of 1 gauge per 500 km2 where a range-dependent adjustment complemented with a static local bias correction performs best.

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

    Science.gov (United States)

    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.

  2. Estimating phytoplankton photosynthesis by active fluorescence

    Energy Technology Data Exchange (ETDEWEB)

    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.

  3. Estimating phytoplankton photosynthesis by active fluorescence

    Energy Technology Data Exchange (ETDEWEB)

    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.

  4. The impacts of climatological adjustment of quantitative precipitation estimates on the accuracy of flash flood detection

    Science.gov (United States)

    Zhang, Yu; Reed, Sean; Gourley, Jonathan J.; Cosgrove, Brian; Kitzmiller, David; Seo, Dong-Jun; Cifelli, Robert

    2016-10-01

    The multisensor Quantitative Precipitation Estimates (MQPEs) created by the US National Weather Service (NWS) are subject to a non-stationary bias. This paper quantifies the impacts of climatological adjustment of MQPEs alone, as well as the compound impacts of adjustment and model calibration, on the accuracy of simulated flood peak magnitude and that in detecting flood events. Our investigation is based on 19 watersheds in the mid-Atlantic region of US, which are grouped into small (500 km2) watersheds. NWS archival MQPEs over 1997-2013 for this region are adjusted to match concurrent gauge-based monthly precipitation accumulations. Then raw and adjusted MQPEs serve as inputs to the NWS distributed hydrologic model-threshold frequency framework (DHM-TF). Two experiments via DHM-TF are performed. The first one examines the impacts of adjustment alone through uncalibrated model simulations, whereas the second one focuses on the compound effects of adjustment and calibration on the detection of flood events. Uncalibrated model simulations show broad underestimation of flood peaks for small watersheds and overestimation those for large watersheds. Prior to calibration, adjustment alone tends to reduce the magnitude of simulated flood peaks for small and large basins alike, with 95% of all watersheds experienced decline over 2004-2013. A consequence is that a majority of small watersheds experience no improvement, or deterioration in bias (0% of basins experiencing improvement). By contrast, most (73%) of larger ones exhibit improved bias. Outcomes of the detection experiment show that the role of adjustment is not diminished by calibration for small watersheds, with only 25% of which exhibiting reduced bias after adjustment with calibrated parameters. Furthermore, it is shown that calibration is relatively effective in reducing false alarms (e.g., false alarm rate is down from 0.28 to 0.19 after calibration for small watersheds with calibrated parameters); but its

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

    Science.gov (United States)

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

    2016-10-01

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

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

    Science.gov (United States)

    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. Activities on covariance estimation in Japanese Nuclear Data Committee

    Energy Technology Data Exchange (ETDEWEB)

    Shibata, Keiichi [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    1997-03-01

    Described are activities on covariance estimation in the Japanese Nuclear Data Committee. Covariances are obtained from measurements by using the least-squares methods. A simultaneous evaluation was performed to deduce covariances of fission cross sections of U and Pu isotopes. A code system, KALMAN, is used to estimate covariances of nuclear model calculations from uncertainties in model parameters. (author)

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

    Science.gov (United States)

    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

    Speed regulations of watercraft in protected areas are designed to reduce lethal collisions with wildlife but can have economic consequences. We present a quantitative framework for investigating the risk of deadly collisions between boats and wildlife.

  9. Comparison of Accelerometry Methods for Estimating Physical Activity.

    Science.gov (United States)

    Kerr, Jacqueline; Marinac, Catherine R; Ellis, Katherine; Godbole, Suneeta; Hipp, Aaron; Glanz, Karen; Mitchell, Jonathan; Laden, Francine; James, Peter; Berrigan, David

    2017-03-01

    This study aimed to compare physical activity estimates across different accelerometer wear locations, wear time protocols, and data processing techniques. A convenience sample of middle-age to older women wore a GT3X+ accelerometer at the wrist and hip for 7 d. Physical activity estimates were calculated using three data processing techniques: single-axis cut points, raw vector magnitude thresholds, and machine learning algorithms applied to the raw data from the three axes. Daily estimates were compared for the 321 women using generalized estimating equations. A total of 1420 d were analyzed. Compliance rates for the hip versus wrist location only varied by 2.7%. All differences between techniques, wear locations, and wear time protocols were statistically different (P machine-learned algorithm found 74% of participants with 150 min of walking/running per week. The wrist algorithms found 59% and 60% of participants with 150 min of physical activity per week using the raw vector magnitude and machine-learned techniques, respectively. When the wrist device was worn overnight, up to 4% more participants met guidelines. Estimates varied by 52% across techniques and by as much as 41% across wear locations. Findings suggest that researchers should be cautious when comparing physical activity estimates from different studies. Efforts to standardize accelerometry-based estimates of physical activity are needed. A first step might be to report on multiple procedures until a consensus is achieved.

  10. Quantitative analysis of low-density SNP data for parentage assignment and estimation of family contributions to pooled samples.

    Science.gov (United States)

    Henshall, John M; Dierens, Leanne; Sellars, Melony J

    2014-09-02

    While much attention has focused on the development of high-density single nucleotide polymorphism (SNP) assays, the costs of developing and running low-density assays have fallen dramatically. This makes it feasible to develop and apply SNP assays for agricultural species beyond the major livestock species. Although low-cost low-density assays may not have the accuracy of the high-density assays widely used in human and livestock species, we show that when combined with statistical analysis approaches that use quantitative instead of discrete genotypes, their utility may be improved. The data used in this study are from a 63-SNP marker Sequenom® iPLEX Platinum panel for the Black Tiger shrimp, for which high-density SNP assays are not currently available. For quantitative genotypes that could be estimated, in 5% of cases the most likely genotype for an individual at a SNP had a probability of less than 0.99. Matrix formulations of maximum likelihood equations for parentage assignment were developed for the quantitative genotypes and also for discrete genotypes perturbed by an assumed error term. Assignment rates that were based on maximum likelihood with quantitative genotypes were similar to those based on maximum likelihood with perturbed genotypes but, for more than 50% of cases, the two methods resulted in individuals being assigned to different families. Treating genotypes as quantitative values allows the same analysis framework to be used for pooled samples of DNA from multiple individuals. Resulting correlations between allele frequency estimates from pooled DNA and individual samples were consistently greater than 0.90, and as high as 0.97 for some pools. Estimates of family contributions to the pools based on quantitative genotypes in pooled DNA had a correlation of 0.85 with estimates of contributions from DNA-derived pedigree. Even with low numbers of SNPs of variable quality, parentage testing and family assignment from pooled samples are

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

    Science.gov (United States)

    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 digital mammography are not substantially affected by variations in radiation dose; thus, the use of low-dose techniques for the purpose of density estimation may be feasible. (©) RSNA, 2016 Online supplemental material is available for this article.

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

    Science.gov (United States)

    Mager, P P; Rothe, H

    1990-10-01

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

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

    Science.gov (United States)

    Ortel, Terry W.; Spies, Ryan R.

    2015-11-19

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

  14. Bone Structure and Estimated Bone Strength in Obese Patients Evaluated by High-Resolution Peripheral Quantitative Computed Tomography

    DEFF Research Database (Denmark)

    Andersen, Stine; Frederiksen, Katrine Diemer; Hansen, Stinus;

    2014-01-01

    Obesity is associated with high bone mineral density (BMD), but whether obesity-related higher bone mass increases bone strength and thereby protect against fractures is uncertain. We estimated effects of obesity on bone microarchitecture and estimated strength in 36 patients (12 males and 24...... females, age 25-56 years and BMI 33.2-57.6 kg/m(2)) matched with healthy controls (age 25-54 years and BMI 19.5-24.8 kg/m(2)) in regard to gender, menopausal status, age (±6 years) and height (±6 cm) using high resolution peripheral quantitative computed tomography and dual energy X-ray absorptiometry...

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

    Science.gov (United States)

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

    2012-06-01

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

  16. Heat and mass flux estimation of modern seafloor hydrothermal activity

    Institute of Scientific and Technical Information of China (English)

    ZHAI Shikui; WANG Xingtao; YU Zenghui

    2006-01-01

    Research on heat and mass flux yielded by modern seafloor hydrothermal activity is very important, because it is involved not only in the base of ocean environment research, but also in the historical evolution of seawater properties. Currently, estimating heat flux is based on the observation data of hydrothermal smokers, low-temperature diffusive flow and mid-ocean ridge mainly. But there are some faults, for example, there is lack of a concurrent conductive item in estimating the heat flux by smokers and the error between the half-space cooling model and the observation data is too large. So, three kinds of methods are applied to re-estimating the heat flux of hydrothermal activity resepectively, corresponding estimation is 97.359 GW by hydrothermal smoker and diffusive flow, 84.895 GW by hydrothermal plume, and 4.11 TW by exponential attenuation method put forward by this paper. Research on mass flux estimation is relatively rare, the main reason for this is insufficient field observation data. Mass fluxes of different elements are calculated using hydrothermal vent fluid data from the TAG hydrothermal area on the Mid-Atlantic Ridge for the first time. Difference of estimations by different methods reflects the researching extent of hydrothermal activity, and systematically in-situ observation will help to estimate the contribution of hydrothermal activity to ocean chemical environment, ocean circulation and global climate precisely.

  17. Quantitative estimation of the impact of precipitation and human activities on runoff change of the Huangfuchuan River Basin%皇甫川流域降水量和人类活动对径流量变化影响的定量评估

    Institute of Scientific and Technical Information of China (English)

    WANG Suiji; YAN Yunxia; YAN Ming; ZHAO Xiaokun

    2012-01-01

    The runoff of some rivers in the world especially in the arid and semi-arid areas has decreased remarkably with global or regional climate change and enhanced human activities.The runoff decrease in the arid and semi-arid areas of northern China has brought severe problems in livelihoods and ecology.To reveal the variation characteristics,trends of runoff and their influencing factors have been important scientific issues for drainage basin management.The objective of this study was to analyze the variation trends of the runoff and quantitatively assess the contributions of precipitation and human activities to the runoff change in the Huangfuchuan River Basin based on the measured data in 1960-2008.Two inflection points (turning years) of 1979 and 1998 for the accumulative runoff change,and one inflection point of 1979 for the accumulative precipitation change were identified using the methods of accumulative anomaly analysis.The linear relationships between year and accumulative runoff in 1960-1979,1980-1997 and 1998-2008 and between year and accumulative precipitation in 1960-1979 and 1980-2008 were fitted.A new method of slope change ratio of accumulative quantity (SCRAQ) was put forward and used in this study to calculate the contributions of different factors to the runoff change.Taking 1960-1979 as the base period,the contribution rate of the precipitation and human activities to the decreased runoff was 36.43% and 63.57% in 1980-1997,and 16.81% and 83.19% in 1998-2008,respectively.The results will play an important role in the drainage basin management.Moreover,the new method of SCRAQ can be applied in the quantitative evaluation of runoff change and impacts by different factors in the river basin of arid and semi-arid areas.%@@

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

    Science.gov (United States)

    Alexander, Nathalie; Schwameder, Hermann

    2016-04-01

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

  19. Quantitative Estimation of Risks for Production Unit Based on OSHMS and Process Resilience

    Science.gov (United States)

    Nyambayar, D.; Koshijima, I.; Eguchi, H.

    2017-06-01

    Three principal elements in the production field of chemical/petrochemical industry are (i) Production Units, (ii) Production Plant Personnel and (iii) Production Support System (computer system introduced for improving productivity). Each principal element has production process resilience, i.e. a capability to restrain disruptive signals occurred in and out of the production field. In each principal element, risk assessment is indispensable for the production field. In a production facility, the occupational safety and health management system (Hereafter, referred to as OSHMS) has been introduced to reduce a risk of accidents and troubles that may occur during production. In OSHMS, a risk assessment is specified to reduce a potential risk in the production facility such as a factory, and PDCA activities are required for a continual improvement of safety production environments. However, there is no clear statement to adopt the OSHMS standard into the production field. This study introduces a metric to estimate the resilience of the production field by using the resilience generated by the production plant personnel and the result of the risk assessment in the production field. A method for evaluating how OSHMS functions are systematically installed in the production field is also discussed based on the resilience of the three principal elements.

  20. Estimating distributions out of qualitative and (semi)quantitative microbiological contamination data for use in risk assessment.

    Science.gov (United States)

    Busschaert, P; Geeraerd, A H; Uyttendaele, M; Van Impe, J F

    2010-04-15

    A framework using maximum likelihood estimation (MLE) is used to fit a probability distribution to a set of qualitative (e.g., absence in 25 g), semi-quantitative (e.g., presence in 25 g and absence in 1g) and/or quantitative test results (e.g., 10 CFU/g). Uncertainty about the parameters of the variability distribution is characterized through a non-parametric bootstrapping method. The resulting distribution function can be used as an input for a second order Monte Carlo simulation in quantitative risk assessment. As an illustration, the method is applied to two sets of in silico generated data. It is demonstrated that correct interpretation of data results in an accurate representation of the contamination level distribution. Subsequently, two case studies are analyzed, namely (i) quantitative analyses of Campylobacter spp. in food samples with nondetects, and (ii) combined quantitative, qualitative, semiquantitative analyses and nondetects of Listeria monocytogenes in smoked fish samples. The first of these case studies is also used to illustrate what the influence is of the limit of quantification, measurement error, and the number of samples included in the data set. Application of these techniques offers a way for meta-analysis of the many relevant yet diverse data sets that are available in literature and (inter)national reports of surveillance or baseline surveys, therefore increases the information input of a risk assessment and, by consequence, the correctness of the outcome of the risk assessment.

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

    Science.gov (United States)

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

    2016-05-01

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

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

    Science.gov (United States)

    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

  3. Quantitative Estimation of the Velocity of Urbanization in China Using Nighttime Luminosity Data

    Directory of Open Access Journals (Sweden)

    Ting Ma

    2016-01-01

    Full Text Available Rapid urbanization with sizeable enhancements of urban population and built-up land in China creates challenging planning and management issues due to the complexity of both the urban development and the socioeconomic drivers of environmental change. Improved understanding of spatio-temporal characteristics of urbanization processes are increasingly important for investigating urban expansion and environmental responses to corresponding socioeconomic and landscape dynamics. In this study, we present an artificial luminosity-derived index of the velocity of urbanization, defined as the ratio of temporal trend and spatial gradient of mean annual stable nighttime brightness, to estimate the pace of urbanization and consequent changes in land cover in China for the period of 2000–2010. Using the Defense Meteorological Satellite Program–derived time series of nighttime light data and corresponding satellite-based land cover maps, our results show that the geometric mean velocity of urban dispersal at the country level was 0.21 km·yr−1 across 88.58 × 103 km2 urbanizing areas, in which ~23% of areas originally made of natural and cultivated lands were converted to artificial surfaces between 2000 and 2010. The speed of urbanization varies among urban agglomerations and cities with different development stages and urban forms. Particularly, the Yangtze River Delta conurbation shows the fastest (0.39 km·yr−1 and most extensive (16.12 × 103 km2 urban growth in China over the 10-year period. Moreover, if the current velocity holds, our estimates suggest that an additional 13.29 × 103 km2 in land area will be converted to human-built features while high density socioeconomic activities across the current urbanizing regions and urbanized areas will greatly increase from 52.44 × 103 km2 in 2010 to 62.73 × 103 km2 in China’s mainland during the next several decades. Our findings may provide potential insights into the pace of urbanization in

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

    Science.gov (United States)

    Kaya, G I; Gözler, B

    2005-06-01

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

  5. QUANTITATIVE ESTIMATION OF DNA ISOLATED FROM VARIOUS PARTS OF ANNONA SQUAMOSA

    Directory of Open Access Journals (Sweden)

    Soni Himesh

    2011-12-01

    Full Text Available Plants have been one of the important sources of medicines since the beginning of human civilization. There is a growing demand for plant based medicines, health products, pharmaceuticals, food supplements, cosmetics etc. Annona squamosa Linn is a multipurpose tree with edible fruits & is a source one of the medicinal & industrial products. Annona squamosa Linn is used as an antioxidant, antidiabetics, hepatoprotective, cytotoxicactivity, genetoxicity, antitumor activity, antilice agent. It is related to contain alkaloids, flavonoids, carbohydrates, fixed oils, tannins & phenolic. Genetic variation is essential for long term survival of species and it is a critical feature in conservation. For efficient conservation and management, the genetic composition of the species in different geographic locations needs to be assessed. Plants are attracting more attention among contemporary pharmacy scientists because some human diseases resulting from antibiotic resistance have gained worldwide concern. A number of methods are available and are being developed for the isolation of nucleic acids from plants. The different parts of Annona squamosa were studied for their nucleic acid content by using spectrophotometric analysis. In order to measure DNA content of the Leaves,friuts and stems of Annona squamosa, Spectrophotometry serves various advantages i.e. non-destructive and allows the sample to be recovered for further analysis or manipulation. Spectrophotometry uses the fact that there is a relationship between the absorption of ultraviolet light by DNA/RNA and its concentration in a sample. This article deals with modern approaches to develop a simple, efficient, reliable and cost-effective method for isolation, separation and estimation of total genomic DNA from various parts of the same species.

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

    Science.gov (United States)

    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.

  7. Antitumor activity of 3,4-ethylenedioxythiophene derivatives and quantitative structure-activity relationship analysis

    Science.gov (United States)

    Jukić, Marijana; Rastija, Vesna; Opačak-Bernardi, Teuta; Stolić, Ivana; Krstulović, Luka; Bajić, Miroslav; Glavaš-Obrovac, Ljubica

    2017-04-01

    The aim of this study was to evaluate nine newly synthesized amidine derivatives of 3,4- ethylenedioxythiophene (3,4-EDOT) for their cytotoxic activity against a panel of human cancer cell lines and to perform a quantitative structure-activity relationship (QSAR) analysis for the antitumor activity of a total of 27 3,4-ethylenedioxythiophene derivatives. Induction of apoptosis was investigated on the selected compounds, along with delivery options for the optimization of activity. The best obtained QSAR models include the following group of descriptors: BCUT, WHIM, 2D autocorrelations, 3D-MoRSE, GETAWAY descriptors, 2D frequency fingerprint and information indices. Obtained QSAR models should be relieved in elucidation of important physicochemical and structural requirements for this biological activity. Highly potent molecules have a symmetrical arrangement of substituents along the x axis, high frequency of distance between N and O atoms at topological distance 9, as well as between C and N atoms at topological distance 10, and more C atoms located at topological distances 6 and 3. Based on the conclusion given in the QSAR analysis, a new compound with possible great activity was proposed.

  8. Junction temperature estimation for an advanced active power cycling test

    DEFF Research Database (Denmark)

    Choi, Uimin; Blaabjerg, Frede; Jørgensen, S.

    2015-01-01

    estimation method using on-state VCE for an advanced active power cycling test is proposed. The concept of the advanced power cycling test is explained first. Afterwards the junction temperature estimation method using on-state VCE and current is presented. Further, the method to improve the accuracy......On-state collector-emitter voltage (VCE) is a good indicator to determine the wear-out condition of power device modules. Further, it is a one of the Temperature Sensitive Electrical Parameters (TSEPs) and thus can be used for junction temperature estimation. In this paper, the junction temperature...

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

    Energy Technology Data Exchange (ETDEWEB)

    Beck, B.D.; Toole, A.P.; Callahan, B.G.; Siddhanti, S.K. (Gradient Corporation, Cambridge, MA (United States))

    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.

  10. Validation and measurement uncertainty estimation in food microbiology: differences between quantitative and qualitative methods

    Directory of Open Access Journals (Sweden)

    Vesna Režić Dereani

    2010-09-01

    Full Text Available The aim of this research is to describe quality control procedures, procedures for validation and measurement uncertainty (MU determination as an important element of quality assurance in food microbiology laboratory for qualitative and quantitative type of analysis. Accreditation is conducted according to the standard ISO 17025:2007. General requirements for the competence of testing and calibration laboratories, which guarantees the compliance with standard operating procedures and the technical competence of the staff involved in the tests, recently are widely introduced in food microbiology laboratories in Croatia. In addition to quality manual introduction, and a lot of general documents, some of the most demanding procedures in routine microbiology laboratories are measurement uncertainty (MU procedures and validation experiment design establishment. Those procedures are not standardized yet even at international level, and they require practical microbiological knowledge, altogether with statistical competence. Differences between validation experiments design for quantitative and qualitative food microbiology analysis are discussed in this research, and practical solutions are shortly described. MU for quantitative determinations is more demanding issue than qualitative MU calculation. MU calculations are based on external proficiency testing data and internal validation data. In this paper, practical schematic descriptions for both procedures are shown.

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

    OpenAIRE

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

    2010-01-01

    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 t...

  12. Ultrasonic 3-D vector flow method for quantitative in vivo peak velocity and flow rate estimation

    DEFF Research Database (Denmark)

    Holbek, Simon; Ewertsen, Caroline; Bouzari, Hamed;

    2017-01-01

    Current clinical ultrasound systems are limited to show blood flow movement in either 1-D or 2-D. In this paper, a method for estimating 3-D vector velocities in a plane using the Transverse Oscillation (TO) method, a 32 x 32 element matrix array, and the experimental ultrasound scanner SARUS...... is presented. The aim of this paper is to estimate precise flow rates and peak velocities derived from 3-D vector flow estimates. The emission sequence provides 3-D vector flow estimates at up to 1.145 frames per second in a plane, and was used to estimate 3-D vector flow in a cross sectional image plane....... The method is validated in two phantom studies, where flow rates are measured in a flow-rig, providing a constant parabolic flow, and in a straight-vessel phantom (ø = 8 mm) connected to a flow pump capable of generating time varying waveforms. Flow rates are estimated to be 82.1 ± 2.8 L/min in the flow...

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

    Science.gov (United States)

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

    1998-12-01

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

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

    Science.gov (United States)

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

    2013-04-10

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

  15. Rapid end-point quantitation of prion seeding activity with sensitivity comparable to bioassays.

    Directory of Open Access Journals (Sweden)

    Jason M Wilham

    Full Text Available A major problem for the effective diagnosis and management of prion diseases is the lack of rapid high-throughput assays to measure low levels of prions. Such measurements have typically required prolonged bioassays in animals. Highly sensitive, but generally non-quantitative, prion detection methods have been developed based on prions' ability to seed the conversion of normally soluble protease-sensitive forms of prion protein to protease-resistant and/or amyloid fibrillar forms. Here we describe an approach for estimating the relative amount of prions using a new prion seeding assay called real-time quaking induced conversion assay (RT-QuIC. The underlying reaction blends aspects of the previously described quaking-induced conversion (QuIC and amyloid seeding assay (ASA methods and involves prion-seeded conversion of the alpha helix-rich form of bacterially expressed recombinant PrP(C to a beta sheet-rich amyloid fibrillar form. The RT-QuIC is as sensitive as the animal bioassay, but can be accomplished in 2 days or less. Analogous to end-point dilution animal bioassays, this approach involves testing of serial dilutions of samples and statistically estimating the seeding dose (SD giving positive responses in 50% of replicate reactions (SD(50. Brain tissue from 263K scrapie-affected hamsters gave SD(50 values of 10(11-10(12/g, making the RT-QuIC similar in sensitivity to end-point dilution bioassays. Analysis of bioassay-positive nasal lavages from hamsters affected with transmissible mink encephalopathy gave SD(50 values of 10(3.5-10(5.7/ml, showing that nasal cavities release substantial prion infectivity that can be rapidly detected. Cerebral spinal fluid from 263K scrapie-affected hamsters contained prion SD(50 values of 10(2.0-10(2.9/ml. RT-QuIC assay also discriminated deer chronic wasting disease and sheep scrapie brain samples from normal control samples. In principle, end-point dilution quantitation can be applied to many types of

  16. ESTIMATION OF ACTIVATED ENERGY OF DESORPTION OF n—HEXANE ON ACTIVATED CARBONS BY PTD TECHNIQUE

    Institute of Scientific and Technical Information of China (English)

    LIZhong; WANGHongjuan; 等

    2001-01-01

    In this paper,six kinds of activated carbons such as Ag+-activated carbon,Cu2+activated carbon,Fe3+-activated carbon,activated carbon,Ba2+-activated carbon and Ca2+activated carbon were prepared.The model for estimating activated energy of desorption was established.Temperature-programmed desorption(TPD)experiments were conducted to measure the TPD curves of n-hexanol and then estimate the activation energy for desorption of n-hexanol on the activated carbons.Results showed that the activation energy for the desorption of n-hexanol on the Ag+-activated carbon,the Cu2+-activated carbon and the Fe3+-activated carbon were higher than those of n-hexanol on the activated carbon,the Ca2+-activated carbon and the Ba2+-activated carbon.

  17. ESTIMATION OF ACTIVATED ENERGY OF DESORPTION OF n-HEXANE ON ACTIVATED CARBONS BY TPD TECHNIQUE

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    In this paper, six kinds of activated carbons such as Ag+-activated carbon, Cu2+-activated carbon, Fe3+- activated carbon, activated carbon, Ba2+- activated carbon and Ca2+-activated carbon were prepared. The model for estimating activated energy of desorption was established. Temperature-programmed desorption (TPD) experiments were conducted to measure the TPD curves of n-hexanol and then estimate the activation energy for desorption of n-hexanol on the activated carbons. Results showed that the activation energy for the desorption of n-hexanol on the Ag+- activated carbon, the Cu2+- activated carbon and the Fe3+- activated carbon were higher than those of n-hexanol on the activated carbon, the Ca2+- activated carbon and the Ba2+- activated carbon.

  18. Extrapolated withdrawal-interval estimator (EWE) algorithm: a quantitative approach to establishing extralabel withdrawal times.

    Science.gov (United States)

    Martín-Jiménez, Tomás; Baynes, Ronald E; Craigmill, Arthur; Riviere, Jim E

    2002-08-01

    The extralabel use of drugs can be defined as the use of drugs in a manner inconsistent with their FDA-approved labeling. The passage of the Animal Medicinal Drug Use Clarification Act (AMDUCA) in 1994 and its implementation by the FDA-Center for Veterinary Medicine in 1996 has allowed food animal veterinarians to use drugs legally in an extralabel manner, as long as an appropriate withdrawal period is established. The present study introduces and validates with simulated and experimental data the Extrapolated Withdrawal-Period Estimator (EWE) Algorithm, a procedure aimed at predicting extralabel withdrawal intervals (WDIs) based on the label and pharmacokinetic literature data contained in the Food Animal Residue Avoidance Databank (FARAD). This is the initial and first attempt at consistently obtaining WDI estimates that encompass a reasonable degree of statistical soundness. Data on the determination of withdrawal times after the extralabel use of the antibiotic oxytetracycline were obtained both with simulated disposition data and from the literature. A withdrawal interval was computed using the EWE Algorithm for an extralabel dose of 25 mg/kg (simulation study) and for a dose of 40 mg/kg (literature data). These estimates were compared with the withdrawal times computed with the simulated data and with the literature data, respectively. The EWE estimates of WDP for a simulated extralabel dose of 25 mg/kg was 39 days. The withdrawal time (WDT) obtained for this dose on a tissue depletion study was 39 days. The EWE estimate of WDP for an extralabel intramuscular dose of 40 mg/kg in cattle, based on the kinetic data contained in the FARAD database, was 48 days. The withdrawal time experimentally obtained for similar use of this drug was 49 days. The EWE Algorithm can obtain WDI estimates that encompass the same degree of statistical soundness as the WDT estimates, provided that the assumptions of the approved dosage regimen hold for the extralabel dosage regimen

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

    Science.gov (United States)

    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.

  20. Improved TLC Bioautographic Assay for Qualitative and Quantitative Estimation of Tyrosinase Inhibitors in Natural Products.

    Science.gov (United States)

    Zhou, Jinge; Tang, Qingjiu; Wu, Tao; Cheng, Zhihong

    2017-03-01

    TLC bioautography for tyrosinase inhibitors has made recent progress; however, an assay with a relative low consumption of enzyme and quantitative capability would greatly advance the efficacy of related TLC bioautographic assays. An improved TLC bioautographic assay for detecting tyrosinase inhibitors was developed and validated in this study. L-DOPA (better water-solubility than L-tyrosine) was used as the substrate instead of reported L-tyrosine. The effects of enzyme and substrate concentrations, reaction temperatures and times, and pH values of the reaction system as well as different plate types on the TLC bioautographic assay were optimised. The quantitative analysis was conducted by densitometric scanning of spot areas, and expressed as the relative tyrosinase inhibitory capacity (RTIC) using a positive control (kojic acid) equivalent. The limit of detection (LOD) of this assay was 1.0 ng for kojic acid. This assay has acceptable accuracy (101.73-102.90%), intra- and inter-day, and intra- and inter-plate precisions [relative standard deviation (RSD), less than 7.0%], and ruggedness (RSD, less than 3.5%). The consumption of enzyme (75 U/mL) is relatively low. Two tyrosinase inhibitory compounds including naringenin and 1-O-β-D-glucopyranosyl-4-allylbenzene have been isolated from Rhodiola sacra guided by this TLC bioautographic assay. Our improved assay is a relatively low-cost, sensitive, and quantitative method compared to the reported TLC bioautographic assays. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  1. Statistical estimation of correlated genome associations to a quantitative trait network.

    Directory of Open Access Journals (Sweden)

    Seyoung Kim

    2009-08-01

    Full Text Available Many complex disease syndromes, such as asthma, consist of a large number of highly related, rather than independent, clinical or molecular phenotypes. This raises a new technical challenge in identifying genetic variations associated simultaneously with correlated traits. In this study, we propose a new statistical framework called graph-guided fused lasso (GFlasso to directly and effectively incorporate the correlation structure of multiple quantitative traits such as clinical metrics and gene expressions in association analysis. Our approach represents correlation information explicitly among the quantitative traits as a quantitative trait network (QTN and then leverages this network to encode structured regularization functions in a multivariate regression model over the genotypes and traits. The result is that the genetic markers that jointly influence subgroups of highly correlated traits can be detected jointly with high sensitivity and specificity. While most of the traditional methods examined each phenotype independently and combined the results afterwards, our approach analyzes all of the traits jointly in a single statistical framework. This allows our method to borrow information across correlated phenotypes to discover the genetic markers that perturb a subset of the correlated traits synergistically. Using simulated datasets based on the HapMap consortium and an asthma dataset, we compared the performance of our method with other methods based on single-marker analysis and regression-based methods that do not use any of the relational information in the traits. We found that our method showed an increased power in detecting causal variants affecting correlated traits. Our results showed that, when correlation patterns among traits in a QTN are considered explicitly and directly during a structured multivariate genome association analysis using our proposed methods, the power of detecting true causal SNPs with possibly pleiotropic

  2. THE QUADRANTS METHOD TO ESTIMATE QUANTITATIVE VARIABLES IN MANAGEMENT PLANS IN THE AMAZON

    Directory of Open Access Journals (Sweden)

    Gabriel da Silva Oliveira

    2015-12-01

    Full Text Available This work aimed to evaluate the accuracy in estimates of abundance, basal area and commercial volume per hectare, by the quadrants method applied to an area of 1.000 hectares of rain forest in the Amazon. Samples were simulated by random and systematic process with different sample sizes, ranging from 100 to 200 sampling points. The amounts estimated by the samples were compared with the parametric values recorded in the census. In the analysis we considered as the population all trees with diameter at breast height equal to or greater than 40 cm. The quadrants method did not reach the desired level of accuracy for the variables basal area and commercial volume, overestimating the observed values recorded in the census. However, the accuracy of the estimates of abundance, basal area and commercial volume was satisfactory for applying the method in forest inventories for management plans in the Amazon.

  3. Quantitative Structure-activity Relationship of TIBO HIV-1 Inhibitors

    Institute of Scientific and Technical Information of China (English)

    LI Xiao-Hong; ZHANG Rui-Zhou; CHENG Xin-Lu; YANG Xiang-Dong

    2007-01-01

    Density functional theory (DFT) was used to calculate a set of molecular descriptors (properties) for 14 TIBO derivatives with anti-HIV activity. Principal component analysis (PCA) and hierarchical cluster analysis (HCA) were employed in order to reduce dimensionality and investigate which subset of variables should be more effective for classifying TIBO derivatives according to their degree of anti-HIV activity. The PCA showed that the EHOMO, μ, LogP, QA, QB and MR variables are responsible for the separation between compounds with higher and lower anti-HIV activity. The HCA results are similar to those obtained with PCA. By using the chemometric results, four synthetic compounds were analyzed through PCA and HCA and three of them are proposed as active molecules against HIV, which is consistent with the results of clinic experiments. The methodologies of PCA and HCA provide a reliable rule for classifying new TIBO derivatives with anti-HIV activity. The model obtained showed not only statistical significance but also predictive ability.

  4. A Quantitative Structure-Activity Relationships (QSAR Study of Piperine Based Derivatives with Leishmanicidal Activity

    Directory of Open Access Journals (Sweden)

    Edilson Beserra Alencar Filho

    2017-04-01

    Full Text Available Leishmaniasis is a parasitic disease which represents a serious public health problem in developing countries. It is considered a neglected tropical disease, for which there is little initiative in the search for therapeutic alternatives by pharmaceutical industry. Natural products remain a great source of inspiration for obtaining bioactive molecules. In 2010, Singh and co-workers published the synthesis and in vitro biological activity of piperoyl-aminoacid conjugates, as well as of piperine, against cellular cultures of Leishmania donovani. The piperine is an alkaloid isolated from Piper nigrum that has many activities described in the literature. In this work, we present a Quantitative Structure-Activity Study of piperine derivatives tested by Singh and co-workers, aiming to highlight important molecular features for leishmanicidal activity, obtaining a mathematical model to predict the activity of new analogs. Compounds were submitted to a geometry optimization computational procedure at semiempirical level of quantum theory. Molecular descriptors for the set of compounds were calculated by E-Dragon online plataform, followed by a variable selection procedure using Ordered Predictors Selection algorithm. Validation parameters obtained showed that a good QSAR model, based on multiple linear regression, was obtained (R2 = 0.85; Q2 = 0.69, and the following conclusions regarding the structure-activity relationship were elucidated: Compounds with electronegative atoms on different substituent groups of analogs, absence of unsaturation on lateral chain, presence of ester instead of carboxyl, and large volumes (due the presence of additional aromatic rings trends to increase the activity against promastigote forms of leishmania. DOI: http://dx.doi.org/10.17807/orbital.v9i1.893

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  7. Pion Fluctuation in High Energy Collisions - A Chaos-based Quantitative Estimation with Visibility Graph Technique

    CERN Document Server

    Bhaduri, Susmita

    2016-01-01

    We propose a new approach for studying pion fluctuation for deeper understanding of the dynamical process involved, from a perspective of fBm-based complex network analysis method called Visibility graph Analysis. This chaos-based, rigorous, non-linear technique is applied to study the erratic behavior of multipion production in \\textbf{$\\pi^{-}$-Ag/Br} interactions at $350$ GeV. This method can offer reliable results with finite data points. The \\textbf{Power of Scale-freeness of Visibility Graph} denoted by-\\textit{PSVG} is a measure of fractality, which can be used as a quantitative parameter for the assessment of the state of a chaotic system. The event-wise fluctuation of the multipion production process can be described by this parameter-\\textit{PSVG}. From the analysis of the \\textit{PSVG} parameter, we can quantitatively confirm that fractal behavior of the particle production process depends on the target excitation and also the fractality decreases with the increase of target excitation.

  8. Human ECG signal parameters estimation during controlled physical activity

    Science.gov (United States)

    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.

  9. Estimating marginal properties of quantitative real-time PCR data using nonlinear mixed models

    DEFF Research Database (Denmark)

    Gerhard, Daniel; Bremer, Melanie; Ritz, Christian

    2014-01-01

    A unified modeling framework based on a set of nonlinear mixed models is proposed for flexible modeling of gene expression in real-time PCR experiments. Focus is on estimating the marginal or population-based derived parameters: cycle thresholds and ΔΔc(t), but retaining the conditional mixed mod...

  10. Quantitative estimates of reaction induced pressures: an example from the Norwegian Caledonides.

    Science.gov (United States)

    Vrijmoed, Johannes C.; Podladchikov, Yuri Y.

    2013-04-01

    Estimating the pressure and temperature of metamorphic rocks is fundamental to the understanding of geodynamics. It is therefore important to determine the mechanisms that were responsible for the pressure and temperature obtained from metamorphic rocks. Both pressure and temperature increase with depth in the Earth. Whereas temperature can vary due to local heat sources such as magmatic intrusions, percolation of hot fluids or deformation in shear zones, pressure in petrology is generally assumed to vary homogeneously with depth. However, fluid injection into veins, development of pressure shadows around porphyroblasts, fracturing and folding of rocks all involve variations in stress and therefore also in pressure (mean stress). Volume change during phase transformations or mineral reactions have the potential to build pressure if they proceed faster than the minerals or rocks can deform to accommodate the volume change. This mechanism of pressure generation does not require the rocks to be under differential stress, it may lead however to the development of local differential stress. The Western Gneiss Region (WGR) is a basement window within the Norwegian Caledonides. This area is well known for its occurrences of HP to UHP rocks, mainly found as eclogite boudins and lenses and more rarely within felsic gneisses. Present observations document a regional metamorphic gradient increasing towards the NW, and structures in the field can account for the exhumation of the (U)HP rocks from ~2.5 to 3 GPa. Locally however, mineralogical and geothermobarometric evidence points to metamorphic pressure up to 4 GPa. These locations present an example of local extreme pressure excursions from the regional and mostly coherent metamorphic gradient that are difficult to account for by present day structural field observations. Detailed structural, petrological, mineralogical, geochemical and geochronological study at the Svartberget UHP diamond locality have shown the injection

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

    Science.gov (United States)

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

    2016-10-01

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

  12. State space approach for joint estimation of activity and attenuation map from PET emission sinograms

    Institute of Scientific and Technical Information of China (English)

    Liu Huafeng; You Hongshun; Shi Pengcheng

    2007-01-01

    Quantitative estimation of radioactivity map has important clinical implications for better diagnosis and understanding of cancers. Although attenuation map and activity map are usually treated sequentially, they can obviously benefit a great deal when the transmission data is missing. In this paper, we propose a novel scheme of simultaneously solving for attenuation map and activity distribution from emission sinograms. Our strategy combines the measurement model of PET, and the attenuation parameters are treated as random variables with known prior statistics. After the conversion to state space representation, the extended Kalman filtering procedures are adopted to linearize the equations and to provide the joint estimates in an approximate optimal sense. Experiments have been performed on both synthetic data to illustrate its abilities and benefits.

  13. Evaluation of two "integrated" polarimetric Quantitative Precipitation Estimation (QPE) algorithms at C-band

    Science.gov (United States)

    Tabary, Pierre; Boumahmoud, Abdel-Amin; Andrieu, Hervé; Thompson, Robert J.; Illingworth, Anthony J.; Le Bouar, Erwan; Testud, Jacques

    2011-08-01

    SummaryTwo so-called "integrated" polarimetric rate estimation techniques, ZPHI ( Testud et al., 2000) and ZZDR ( Illingworth and Thompson, 2005), are evaluated using 12 episodes of the year 2005 observed by the French C-band operational Trappes radar, located near Paris. The term "integrated" means that the concentration parameter of the drop size distribution is assumed to be constant over some area and the algorithms retrieve it using the polarimetric variables in that area. The evaluation is carried out in ideal conditions (no partial beam blocking, no ground-clutter contamination, no bright band contamination, a posteriori calibration of the radar variables ZH and ZDR) using hourly rain gauges located at distances less than 60 km from the radar. Also included in the comparison, for the sake of benchmarking, is a conventional Z = 282 R1.66 estimator, with and without attenuation correction and with and without adjustment by rain gauges as currently done operationally at Météo France. Under those ideal conditions, the two polarimetric algorithms, which rely solely on radar data, appear to perform as well if not better, pending on the measurements conditions (attenuation, rain rates, …), than the conventional algorithms, even when the latter take into account rain gauges through the adjustment scheme. ZZDR with attenuation correction is the best estimator for hourly rain gauge accumulations lower than 5 mm h -1 and ZPHI is the best one above that threshold. A perturbation analysis has been conducted to assess the sensitivity of the various estimators with respect to biases on ZH and ZDR, taking into account the typical accuracy and stability that can be reasonably achieved with modern operational radars these days (1 dB on ZH and 0.2 dB on ZDR). A +1 dB positive bias on ZH (radar too hot) results in a +14% overestimation of the rain rate with the conventional estimator used in this study (Z = 282R1.66), a -19% underestimation with ZPHI and a +23

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  16. Study on Correlation and Quantitative Error Estimation Method Among the Splitting Shear Wave Identification Methods

    Institute of Scientific and Technical Information of China (English)

    Liu Xiqiang; Zhou Huilan; Li Hong; Gai Dianguang

    2000-01-01

    Based on the propagation characteristics of shear wave in the anisotropic layers, thecorrelation among several splitting shear-wave identification methods hasbeen studied. Thispaper puts forward the method estimating splitting shear-wave phases and its reliability byusing of the assumption that variance of noise and useful signal data obey normaldistribution. To check the validity of new method, the identification results and errorestimation corresponding to 95% confidence level by analyzing simulation signals have beengiven.

  17. A quantitative method for estimating cloud cover over tropical cyclones from satellite data

    OpenAIRE

    BALOGUN, E. E.

    2011-01-01

    A photometric method for quantifying cloud cover over tropical cyclones as observed from satellite photographs is presented. Two gridded photographs of tropical cyclones are analyzed by this method. On each photograph, nine concentric circles are drawn. The observed or reported centre of the cyclones is used as the centre for each set of concentric circles. Photometric estimates of cloud cover are made along the nine concentric circles. The principle of harmonic analysis is applied to the cl...

  18. [Non-parametric Bootstrap estimation on the intraclass correlation coefficient generated from quantitative hierarchical data].

    Science.gov (United States)

    Liang, Rong; Zhou, Shu-dong; Li, Li-xia; Zhang, Jun-guo; Gao, Yan-hui

    2013-09-01

    This paper aims to achieve Bootstraping in hierarchical data and to provide a method for the estimation on confidence interval(CI) of intraclass correlation coefficient(ICC).First, we utilize the mixed-effects model to estimate data from ICC of repeated measurement and from the two-stage sampling. Then, we use Bootstrap method to estimate CI from related ICCs. Finally, the influences of different Bootstraping strategies to ICC's CIs are compared. The repeated measurement instance show that the CI of cluster Bootsraping containing the true ICC value. However, when ignoring the hierarchy characteristics of data, the random Bootsraping method shows that it has the invalid CI. Result from the two-stage instance shows that bias observed between cluster Bootstraping's ICC means while the ICC of the original sample is the smallest, but with wide CI. It is necessary to consider the structure of data as important, when hierarchical data is being resampled. Bootstrapping seems to be better on the higher than that on lower levels.

  19. 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)

    Science.gov (United States)

    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.

  20. H.264 MOTION ESTIMATION ALGORITHM BASED ON VIDEO SEQUENCES ACTIVITY

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Motion estimation is an important part of H.264/AVC encoding progress, with high computational complexity. Therefore, it is quite necessary to find a fast motion estimation algorithm for real-time applications. The algorithm proposed in this letter adjudges the macroblocks activity degree first; then classifies different video sequences, and applies different search strategies according to the result. Experiments show that this method obtains almost the same video quality with the Full Search (FS) algorithm but with reduced more than 95% computation cost.

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

    Science.gov (United States)

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

    2012-01-01

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

  2. Quantitative assessment of soil parameter (KD and TC) estimation using DGT measurements and the 2D DIFS model.

    Science.gov (United States)

    Lehto, N J; Sochaczewski, L; Davison, W; Tych, W; Zhang, H

    2008-03-01

    Diffusive gradients in thin films (DGT) is a dynamic, in situ measuring technique that can be used to supply diverse information on concentrations and behaviour of solutes. When deployed in soils and sediments, quantitative interpretation of DGT measurements requires the use of a numerical model. An improved version of the DGT induced fluxes in soils and sediments model (DIFS), working in two dimensions (2D DIFS), was used to investigate the accuracy with which DGT measurements can be used to estimate the distribution coefficient for labile metal (KD) and the response time of the soil to depletion (TC). The 2D DIFS model was used to obtain values of KD and TC for Cd, Zn and Ni in three different soils, which were compared to values determined previously using 1D DIFS for these cases. While the 1D model was shown to provide reasonable estimates of KD, the 2D model refined the estimates of the kinetic parameters. Desorption rate constants were shown to be similar for all three metals and lower than previously thought. Calculation of an error function as KD and TC are systematically varied showed the spread of KD and TC values that fit the experimental data equally well. These automatically generated error maps reflected the quality of the data and provided an appraisal of the accuracy of parameter estimation. They showed that in some cases parameter accuracy could be improved by fitting the model to a sub-set of data.

  3. Estimation of the Accuracy of Method for Quantitative Determination of Volatile Compounds in Alcohol Products

    CERN Document Server

    Charepitsa, S V; Zadreyko, Y V; Sytova, S N

    2016-01-01

    Results of the estimation of the precision for determination volatile compounds in alcohol-containing products by gas chromatography: acetaldehyde, methyl acetate, ethyl acetate, methanol, isopropyl alcohol, propyl alcohol, isobutyl alcohol, butyl alcohol, isoamyl alcohol are presented. To determine the accuracy, measurements were planned in accordance with ISO 5725 and held at the gas chromatograph Crystal-5000. Standard deviation of repeatability, intermediate precision and their limits are derived from obtained experimental data. The uncertainty of the measurements was calculated on the base of an "empirical" method. The obtained values of accuracy indicate that the developed method allows measurement uncertainty extended from 2 to 20% depending on the analyzed compound and measured concentration.

  4. Spectrophotometric Quantitative Estimation and Validation of Nimesulide and Drotaverine Hydrochloride in Tablet Dosage form

    OpenAIRE

    Prasad R. K.; Sharma R

    2010-01-01

    Three simple, sensitive and accurate UV spectrophotometric methods, I; first order derivative spectrophotometric, II; area under curve and III; multi-component method, has been developed for the estimation of drotaverine hydrochloride and nimesulide in tablets dosage form. Beers’ law was obeyed in the concentration range 5-35 µgml-1 and 10-50 µgml-1 for drotaverine (λmax = 230.5 nm) and nimesulide (λmax = 331.5 nm) respectively in methanol. All the three methods allowed rapid analysis of bina...

  5. Quantitative assessment of target dependence of pion fluctuation in hadronic interactions – estimation through erraticity

    Indian Academy of Sciences (India)

    Dipak Ghosh; Argha Deb; Mitali Mondal; Arindam Mondal; Sitram Pal

    2012-12-01

    Event-to-event fluctuation pattern of pions produced by proton and pion beams is studied in terms of the newly defined erraticity measures $ (p, q)$, $_{q}^{'}$ and $_{q}^{'}$ proposed by Cao and Hwa. The analysis reveals the erratic behaviour of the produced pions signifying the chaotic multiparticle production in high-energy hadron–nucleus interactions (- –AgBr interactions at 350 GeV/c and –AgBr interactions at 400 GeV/c). However, the chaoticity does not depend on whether the projectile is proton or pion. The results are compared with the results of the VENUS-generated data for the above interactions which suggests that VENUS event generator is unable to reproduce the event-to-event fluctuations of spatial patterns of final states. A comparative study of –AgBr interactions and - collisions at 400 GeV/c from NA27, with the help of a quantitative parameter for the assessment of pion fluctuation, indicates conclusively that particle production process is more chaotic for hadron–nucleus interactions than for hadron–hadron interactions.

  6. Noninvasive and quantitative intracranial pressure estimation using ultrasonographic measurement of optic nerve sheath diameter

    Science.gov (United States)

    Wang, Li-juan; Yao, Yan; Feng, Liang-shu; Wang, Yu-zhi; Zheng, Nan-nan; Feng, Jia-chun; Xing, Ying-qi

    2017-01-01

    We aimed to quantitatively assess intracranial pressure (ICP) using optic nerve sheath diameter (ONSD) measurements. We recruited 316 neurology patients in whom ultrasonographic ONSD was measured before lumbar puncture. They were randomly divided into a modeling and a test group at a ratio of 7:3. In the modeling group, we conducted univariate and multivariate analyses to assess associations between ICP and ONSD, age, sex, BMI, mean arterial blood pressure, diastolic blood pressure. We derived the mathematical function “Xing & Wang” from the modelling group to predict ICP and evaluated the function in the test group. In the modeling group, ICP was strongly correlated with ONSD (r = 0.758, p Watson value = 1.94). In the test group, a significant correlation was found between the observed and predicted ICP (r = 0.76, p < 0.001). Bland-Altman analysis yielded a mean difference between measurements of −0.07 ± 41.55 mmH2O. The intraclass correlation coefficient and its 95%CIs for noninvasive ICP assessments using our prediction model was 0.86 (0.79–0.90). Ultrasonographic ONSD measurements provide a potential noninvasive method to quantify ICP that can be conducted at the bedside. PMID:28169341

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

    Directory of Open Access Journals (Sweden)

    H. Peregrina-Barreto

    2014-01-01

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

  8. IMPROVED RP-HPLC METHOD FOR QUANTITATIVE ESTIMATION OF STEVIOSIDE IN STEVIA REBAUDIANA BERTONI BURM

    Directory of Open Access Journals (Sweden)

    Shankar Katekhaye

    2011-01-01

    Full Text Available An RP-HPLC method with UV array detection was established for the determination of stevioside, an extract of herbal S. rebaudiana plant. The stevioside was separated using isocratic solvent system consisting of methanol and 0.1% orthophosphoric acid (v/v in water (70:30 at flow rate of 1.0 ml/min and the detection wavelength of 219 nm. The method was validated for linearity, precision, accuracy, limit of detection (LOD, and limit of quantitation (LOQ. The linearity of the proposed method was obtained in the range of 5.0-75 μg/ml with regression coefficient of 0.9999. Intraday and interday precision studies showed the relative standard deviation less than 2.5%. The accuracy of the proposed method was determined by a recovery study conducted at 3 different levels. The average recovery was 97-99%. The LOD and LOQ were 0.02 and 0.05 µg/ml, respectively. The content of stevioside obtained in the dried leaves powder was within the ranges of 6.83 – 7.91% and 1.7 – 2.9 % w/w, respectively. The proposed method is simple, sensitive, yet reproducible. It is therefore suitable for routine analysis of stevioside in S. rebaudiana Bertoni.

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

    Science.gov (United States)

    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.

  10. Tree Root System Characterization and Volume Estimation by Terrestrial Laser Scanning and Quantitative Structure Modeling

    Directory of Open Access Journals (Sweden)

    Aaron Smith

    2014-12-01

    Full Text Available The accurate characterization of three-dimensional (3D root architecture, volume, and biomass is important for a wide variety of applications in forest ecology and to better understand tree and soil stability. Technological advancements have led to increasingly more digitized and automated procedures, which have been used to more accurately and quickly describe the 3D structure of root systems. Terrestrial laser scanners (TLS have successfully been used to describe aboveground structures of individual trees and stand structure, but have only recently been applied to the 3D characterization of whole root systems. In this study, 13 recently harvested Norway spruce root systems were mechanically pulled from the soil, cleaned, and their volumes were measured by displacement. The root systems were suspended, scanned with TLS from three different angles, and the root surfaces from the co-registered point clouds were modeled with the 3D Quantitative Structure Model to determine root architecture and volume. The modeling procedure facilitated the rapid derivation of root volume, diameters, break point diameters, linear root length, cumulative percentages, and root fraction counts. The modeled root systems underestimated root system volume by 4.4%. The modeling procedure is widely applicable and easily adapted to derive other important topological and volumetric root variables.

  11. Quantitative estimation of temperature variations in plantar angiosomes: a study case for diabetic foot.

    Science.gov (United States)

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

    2014-01-01

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

  12. A quantitative structure–activity relationship (QSAR study of peptide drugs based on a new descriptor of amino acids

    Directory of Open Access Journals (Sweden)

    Tong Jian-Bo

    2015-01-01

    Full Text Available Quantitative structure-activity relationships (QSAR approach is used for finding the relationship between molecular structures and the activity of peptide drugs. In this work, stepwise multiple regression, was employed to select optimal subset of descriptors that have significant contribution to the drug activity of 21 oxytocin analogues, 48 bitter tasting threshold, and 58 angiotensin-converting enzyme inhibitors. A new set of descriptor, SVWGM, was used for the prediction of the drug activity of peptide drugs and then were used to build the model by partial least squares method, for it’s estimation stability and generalization ability was strictly analyzed by both internal and external validations, with cross-validation correlation coefficient, correlation coefficient and correlation coefficient of external validation.

  13. Integral quantification accuracy estimation for reporter ion-based quantitative proteomics (iQuARI).

    Science.gov (United States)

    Vaudel, Marc; Burkhart, Julia M; Radau, Sonja; Zahedi, René P; Martens, Lennart; Sickmann, Albert

    2012-10-05

    With the increasing popularity of comparative studies of complex proteomes, reporter ion-based quantification methods such as iTRAQ and TMT have become commonplace in biological studies. Their appeal derives from simple multiplexing and quantification of several samples at reasonable cost. This advantage yet comes with a known shortcoming: precursors of different species can interfere, thus reducing the quantification accuracy. Recently, two methods were brought to the community alleviating the amount of interference via novel experimental design. Before considering setting up a new workflow, tuning the system, optimizing identification and quantification rates, etc. one legitimately asks: is it really worth the effort, time and money? The question is actually not easy to answer since the interference is heavily sample and system dependent. Moreover, there was to date no method allowing the inline estimation of error rates for reporter quantification. We therefore introduce a method called iQuARI to compute false discovery rates for reporter ion based quantification experiments as easily as Target/Decoy FDR for identification. With it, the scientist can accurately estimate the amount of interference in his sample on his system and eventually consider removing shadows subsequently, a task for which reporter ion quantification might not be the solution of choice.

  14. Quantitative Population Epigenetics in Screening and Development of Regulator-Active Factors of the Farming System

    OpenAIRE

    Stauss, R.

    2013-01-01

    Likewise, index selection based on statistical genetic theory in plant and animal breeding the methodology "Quantitative Population Epigenetics" can be appropriated to improve efficiency in screening and development of regulator-active factors of the farming system for potential to enhance quantitative characters such as yield, standability and resistance to unfavorable environmental influences (e.g., water stress, cold temperatures, disease resistance). For example, as was shown for an ef...

  15. Impact of high (131)I-activities on quantitative (124)I-PET

    DEFF Research Database (Denmark)

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

    2015-01-01

    relevant [Formula: see text]I/[Formula: see text]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...... [Formula: see text]I-activities was good and image quantification unaffected except at very high count rates. Quantitation accuracy and contrast recovery were uninfluenced at [Formula: see text]I-activities below 1000 MBq, whereas image noise was slightly increased. The NECR peaked at 550 MBq of [Formula...

  16. Age estimation during the blow fly intra-puparial period: a qualitative and quantitative approach using micro-computed tomography.

    Science.gov (United States)

    Martín-Vega, Daniel; Simonsen, Thomas J; Wicklein, Martina; Hall, Martin J R

    2017-05-04

    Minimum post-mortem interval (minPMI) estimates often rely on the use of developmental data from blow flies (Diptera: Calliphoridae), which are generally the first colonisers of cadavers and, therefore, exemplar forensic indicators. Developmental data of the intra-puparial period are of particular importance, as it can account for more than half of the developmental duration of the blow fly life cycle. During this period, the insect undergoes metamorphosis inside the opaque, barrel-shaped puparium, formed by the hardening and darkening of the third instar larval cuticle, which shows virtually no external changes until adult emergence. Regrettably, estimates based on the intra-puparial period are severely limited due to the lack of reliable, non-destructive ageing methods and are frequently based solely on qualitative developmental markers. In this study, we use non-destructive micro-computed tomography (micro-CT) for (i) performing qualitative and quantitative analyses of the morphological changes taking place during the intra-puparial period of two forensically relevant blow fly species, Calliphora vicina and Lucilia sericata, and (ii) developing a novel and reliable method for estimating insect age in forensic practice. We show that micro-CT provides age-diagnostic qualitative characters for most 10% time intervals of the total intra-puparial period, which can be used over a range of temperatures and with a resolution comparable to more invasive and time-consuming traditional imaging techniques. Moreover, micro-CT can be used to yield a quantitative measure of the development of selected organ systems to be used in combination with qualitative markers. Our results confirm micro-CT as an emerging, powerful tool in medico-legal investigations.

  17. New Descriptors of Amino Acids and Its Applications to Peptide Quantitative Structure-activity Relationship

    Institute of Scientific and Technical Information of China (English)

    SHU Mao; HUO Dan-Qun; MEI Hua; LIANG Gui-Zhao; ZHANG Mei; LI Zhi-Liang

    2008-01-01

    A new set of descriptors, HSEHPCSV (component score vector of hydrophobic, steric, and electronic properties together with hydrogen bonding contributions), were derived from principal component analyses of 95 physicochemical variables of 20 natural amino acids separately according to different kinds of properties described, namely, hydrophobic, steric, and electronic properties as well as hydrogen bonding contributions. HSEHPCSV scales were then employed to express structures of angiotensin-converting enzyme inhibitors, bitter tasting thresholds and bactericidal 18 peptide, and to construct QSAR models based on partial least square (PLS). The results obtained are as follows: the multiple correlation coefficient (R2cum) of 0.846, 0.917 and 0.993, leave-one-out cross validated Q2cum of 0.835, 0.865 and 0.899, and root-mean-square error for estimated error (RMSEE) of 0.396, 0.187and 0.22, respectively. Satisfactory results showed that, as new amino acid scales, data of HSEHPCSV may be a useful structural expression methodology for the studies on peptide QSAR (quantitative structure-activity relationship) due to many advantages such as plentiful structural information, definite physical and chemical meaning and easy interpretation.

  18. Prediction of Toxicity of Phenols and Anilines to Algae by Quantitative Structure-activity Relationship

    Institute of Scientific and Technical Information of China (English)

    GUANG-HUA LU; CHAO WANG; XIAO-LING GUO

    2008-01-01

    Objective To measure the toxicity of phenol, aniline, and their derivatives to algae and to assess, model and predict the toxicity using quantitative structure-activity relationship (QSAR) method. Methods Oxygen production was used as the response endpoint for assessing the toxic effects of chemicals on algal photosynthesis. The energy of the lowest unoccupied molecular orbital (ELUMO) and the energy of the highest occupied molecular orbital (E) Were obtained from the ChemOffice 2004 program using the quantum chemical method MOPAC, and the frontier orbital energy gap (ΔE) was obtained. Results The compounds exhibited a reasonably wide range of algal toxicity. The most toxic compound was α-naphthol, whereas the least toxic one was aniline. A two-descriptor model was derived from the algal toxicity and structural parameters:logl/EC50=0.268logKow-1.006ΔE+11.769 (n=20,r2=0.946). This model was stable and satisfactory for predicting toxicity. Conclusion Phenol aniline, and their derivatives axe polar narcotics. Their toxicity is greater than estimated by hydrophobicity only, and addition of the frontier orbital energy gap ΔE can significantly improve the prediction of logKow-dependont models.

  19. Quantitative structure-activity relationships for green algae growth inhibition by polymer particles.

    Science.gov (United States)

    Nolte, Tom M; Peijnenburg, Willie J G M; Hendriks, A Jan; van de Meent, Dik

    2017-03-19

    After use and disposal of chemical products, many types of polymer particles end up in the aquatic environment with potential toxic effects to primary producers like green algae. In this study, we have developed Quantitative Structure-Activity Relationships (QSARs) for a set of highly structural diverse polymers which are capable to estimate green algae growth inhibition (EC50). The model (N = 43, R(2) = 0.73, RMSE = 0.28) is a regression-based decision tree using one structural descriptor for each of three polymer classes separated based on charge. The QSAR is applicable to linear homo polymers as well as copolymers and does not require information on the size of the polymer particle or underlying core material. Highly branched polymers, non-nitrogen cationic polymers and polymeric surfactants are not included in the model and thus cannot be evaluated. The model works best for cationic and non-ionic polymers for which cellular adsorption, disruption of the cell wall and photosynthesis inhibition were the mechanisms of action. For anionic polymers, specific properties of the polymer and test characteristics need to be known for detailed assessment. The data and QSAR results for anionic polymers, when combined with molecular dynamics simulations indicated that nutrient depletion is likely the dominant mode of toxicity. Nutrient depletion in turn, is determined by the non-linear interplay between polymer charge density and backbone flexibility.

  20. Quantitative estimation of lithofacies from seismic data in a tertiary turbidite system in the North Sea

    Energy Technology Data Exchange (ETDEWEB)

    Joerstad, A.K.; Avseth, P.Aa; Mukerji, T.; Mavko, G.; Granli, J.R.

    1998-12-31

    Deep water clastic systems and associated turbidite reservoirs are often characterized by very complex sand distributions and reservoir description based on conventional seismic and well-log stratigraphic analysis may be very uncertain in these depositional environments. There is shown that reservoirs in turbidite systems have been produced very inefficiently in conventional development. More than 70% of the mobile oil is commonly left behind, because of the heterogeneous nature of these reservoirs. In this study there is examined a turbidite system in the North Sea with five available wells and a 3-D seismic near and far offset stack to establish most likely estimates of facies and pore fluid within the cube. 5 figs.

  1. Estimates of genetic variability and association studies in quantitative plant traits of Eruca spp. landraces

    Directory of Open Access Journals (Sweden)

    Bozokalfa Kadri Mehmet

    2010-01-01

    Full Text Available Despite the increasing of economical importance of rocket plant limited information is available on genetic variability for the agronomic traits among Eruca spp. Hence, heritability and association studies of plant properties are necessities for a successful further rocket breeding programme. The objective of this study was to examine phenotypic and genotypic variability, broad sense heritability, genetic advance, genotypic and phenotypic correlation and mean for agronomic traits of rocket plant. The magnitude of phenotypic coefficient of variation values for all the traits were higher than the corresponding values and broad sense heritability estimates exceeded 65% for all traits. Phenotypic coefficients of variability (PCV ranged from 7.60 to 34.34% and genotypic coefficients of variability (GCV ranged between 5.58% for petiole thickness and 34.30% for plant weight. The results stated that plant weight, siliqua width, seed per siliqua and seed weight could be useful character for improved Eruca spp. breeding programme.

  2. Active Power Deficit Estimation in Presence of Renewable Energy Sources

    DEFF Research Database (Denmark)

    Hoseinzadeh, Bakhtyar; Silva, Filipe Miguel Faria da; Bak, Claus Leth

    2015-01-01

    following outage of SMs during cascading events. Therefore, the active power deficit following the disturbance/s may not be properly estimated by existing conventional System Frequency Response (SFR) methods in which the total inertia of the power system is required to be known. In this paper, the actual......The inertia of the power system is reduced in the presence of Renewable Energy Sources (RESs) due to their low or even no contribution in the inertial response as it is inherently available in the Synchronous Machines (SMs). The total inertia of the grid becomes unknown or at least uncertain...... active power deficit is estimated independent of grid inertia, type and number of occurred cascading events after each Load Shedding (LS) stage using shed load amount, pre-shed and post-shed Rate of Change of Frequency (ROCOF). Numerical simulations conducted on IEEE 39 bus standard test system in Dig...

  3. Activity Recognition Using Biomechanical Model Based Pose Estimation

    OpenAIRE

    Reiss, Attila; Hendeby, Gustaf; Bleser, Gabriele; Stricker, Didier

    2010-01-01

    In this paper, a novel activity recognition method based on signal-oriented and model-based features is presented. The model-based features are calculated from shoulder and elbow joint angles and torso orientation, provided by upper-body pose estimation based on a biomechanical body model. The recognition performance of signal-oriented and model-based features is compared within this paper, and the potential of improving recognition accuracy by combining the two approaches is proved: the accu...

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

    Energy Technology Data Exchange (ETDEWEB)

    Claire, Mark W. [School of Environmental Sciences, University of East Anglia, Norwich, UK NR4 7TJ (United Kingdom); Sheets, John; Meadows, Victoria S. [Virtual Planetary Laboratory and Department of Astronomy, University of Washington, Box 351580, Seattle, WA 98195 (United States); Cohen, Martin [Radio Astronomy Laboratory, University of California, Berkeley, CA 94720-3411 (United States); Ribas, Ignasi [Institut de Ciencies de l' Espai (CSIC-IEEC), Facultat de Ciencies, Torre C5 parell, 2a pl, Campus UAB, E-08193 Bellaterra (Spain); Catling, David C., E-mail: M.Claire@uea.ac.uk [Virtual Planetary Laboratory and Department of Earth and Space Sciences, University of Washington, Box 351310, Seattle, WA 98195 (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Mounsey Kate E

    2012-01-01

    Full Text Available Abstract 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 (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.

  6. A quantitative framework to estimate the relative importance of environment, spatial variation and patch connectivity in driving community composition.

    Science.gov (United States)

    Monteiro, Viviane F; Paiva, Paulo C; Peres-Neto, Pedro R

    2017-03-01

    Perhaps the most widely used quantitative approach in metacommunity ecology is the estimation of the importance of local environment vs. spatial structuring using the variation partitioning framework. Contrary to metapopulation models, however, current empirical studies of metacommunity structure using variation partitioning assume a space-for-dispersal substitution due to the lack of analytical frameworks that incorporate patch connectivity predictors of dispersal dynamics. Here, a method is presented that allows estimating the relative importance of environment, spatial variation and patch connectivity in driving community composition variation within metacommunities. The proposed approach is illustrated by a study designed to understand the factors driving the structure of a soft-bottom marine polychaete metacommunity. Using a standard variation partitioning scheme (i.e. where only environmental and spatial predictors are used), only about 13% of the variation in metacommunity structure was explained. With the connectivity set of predictors, the total amount of explained variation increased up to 51% of the variation. These results highlight the importance of considering predictors of patch connectivity rather than just spatial predictors. Given that information on connectivity can be estimated by commonly available data on species distributions for a number of taxa, the framework presented here can be readily applied to past studies as well, facilitating a more robust evaluation of the factors contributing to metacommunity structure.

  7. Validation of Body Condition Indices and Quantitative Magnetic Resonance in Estimating Body Composition in a Small Lizard

    Science.gov (United States)

    WARNER, DANIEL A.; JOHNSON, MARIA S.; NAGY, TIM R.

    2017-01-01

    Measurements of body condition are typically used to assess an individual’s quality, health, or energetic state. Most indices of body condition are based on linear relationships between body length and mass. Although these indices are simple to obtain, nonlethal, and useful indications of energetic state, their accuracy at predicting constituents of body condition (e.g., fat and lean mass) are often unknown. The objectives of this research were to (1) validate the accuracy of another simple and noninvasive method, quantitative magnetic resonance (QMR), at estimating body composition in a small-bodied lizard, Anolis sagrei, and (2) evaluate the accuracy of two indices of body condition (based on length–mass relationships) at predicting body fat, lean, and water mass. Comparisons of results from QMR scans to those from chemical carcass analysis reveal that QMR measures body fat, lean, and water mass with excellent accuracy in male and female lizards. With minor calibration from regression equations, QMR will be a reliable method of estimating body composition of A. sagrei. Body condition indices were positively related to absolute estimates of each constituent of body composition, but these relationships showed considerable variation around regression lines. In addition, condition indices did not predict fat, lean, or water mass when adjusted for body mass. Thus, our results emphasize the need for caution when interpreting body condition based upon linear measurements of animals. Overall, QMR provides an alternative noninvasive method for accurately measuring fat, lean, and water mass in these small-bodied animals. PMID:28035770

  8. Quantitative estimation of sediment erosion and accretion processes in a micro-tidal coast

    Institute of Scientific and Technical Information of China (English)

    G.Udhaba DORA; V.Sanil KUMAR; P.VINAYARAJ; C.S.PHILIP; G.JOHNSON

    2014-01-01

    Spatio-temporal cross-shore profiles and textural characteristics are the key parameters for understanding dynamics of the inter-tidal sedimentary environment. This study describes short-term dynamics of the inter-tidal sedimentary environment at beaches along the micro-tidal coast. Further a correlation is estimated in cross-shore morphodynamics and textural characteristics of surface sediments. The sedimentary environment is examined for a complete annual cycle using monthly collected cross-shore profiles and sediment samples. The Devbag beach (northern side) and Ravindranath Tagore beach (southern side) at the Kali river mouth, Karwar, west coast of India are characterized from extremely gentle to average slope, and broadly composed of unimodal sands. The sedimentary environment is significantly composed of textures having fine to medium sand, well to moderately sorted, fine to coarse skewed, and platykurtic to leptokurtic in nature. During the annual cycle a reversal pattern is observed between the two adjacent beaches, where a slower rate of sediment accretion is observed at Devbag beach while Ravindranath Tagore beach exhibited erosion. The beach dynamics along with the propagation of south-west (SW) and south-west-west (SWW) waves towards the coast significantly exhibit a dominance of northward sediment transport with the existence of a northerly alongshore current. In addition, the study reveals that an eroded beach may not be significantly identified composed of coarse grains. The poor correlation in morpho-sedimentary characteristics reveals the prediction of grain characteristics based on beach profile and vice-versa is unrealistic.

  9. Hyperspectral Estimation of Corn Fraction of Photosynthetically Active Radiation

    Institute of Scientific and Technical Information of China (English)

    YANG Fei; ZHANG Bai; SONG Kai-shan; WANG Zong-ming; YOU Jin-chun; LIU Dian-wei; XU Jing-ping

    2007-01-01

    Fraction of absorbed photosynthetically active radiation (FPAR) is one of the important variables in many vegetation productivity and biomass estimation models. Therefore, it is significant to retrieve FPAR accurately for the improvement of model precision. On the basis of the field experiment, this article analyzed the correlations between corn canopy FPAR and spectral reflectance, and reflectance derivative. Discussion about the mechanism of FPAR estimation with different empirical models is based upon corn canopy reflectance, reflectance derivative, NDVI (normalized difference vegetation index) and RVI (ratio vegetation index). The reflectance of visible bands showed much better correlations with FPAR than near-infrared bands. The correlation between FPAR and reflectance derivative varied more frequently and greatly than that between FPAR and reflectance, and with preferable correlation only around 520, 570, 670, 805, 950, and 1010 nm.Reflectance and reflectance derivative both had intimate correlation with FPAR at some typical single band, with the maximum R2 of 0.791 and 0.882, respectively. In a word, reflectance derivative and vegetation index were much effective in the estimation of corn FPAR than reflectance, and the stepwise regression of multibands with reflectance derivative showed the best regression with R2 of 0.944. Reflectance at 375 and 950 nm with absorption characteristics caused by water showed prodigious potential for FPAR precisely estimating model establishment. On the whole, vegetation index and reflectance derivative had good relationships with FPAR, and could be used for FAPR estimation. It would be effective for choosing right bands and excavating the hyperspectral data to improve FPAR estimating precision.

  10. [Quantitative topographic characterization of the myoelectric activity distribution of the masseter muscle: mapping of spectral EMG parameters].

    Science.gov (United States)

    Scholle, H C; Schumann, N P; Anders, C; Mey, E

    1992-09-01

    A new method for quantitative characterization of myoelectrical masseter activity distribution by mapping of spectral EMG-parameters is described. The surface electromyograms of M. masseter were monopolarly recorded (16 channels). On the basis of registered EMG intervals (512 ms) the spectral EMG power of several frequency bands was calculated (Fast Fourier Transformation). The spectral EMG parameters between the 16 electrode positions were estimated by linear interpolation (4-nearest neighbours algorithm). Afterwards the spectral EMG parameters were fitted in a grey-tone or colour scale with 10 intervals. The so obtained EMG activity maps ("EMG-Maps") permit a quantitative-topographic characterization of myoelectrical masseter activity during different functional load procedures. The frequency range which is to consider in masseter surface-EMG investigations encloses frequencies between 15 and 500 Hz. The topography of EMG activation pattern of M. masseter is only described in a comprehensive manner when the electrode array consists of 16 electrodes and more. During defined motor tasks like clenching with controlled forces the reproducibility of EMG-Maps which respect to the topography of EMG activity pattern is very high. The absolute values of spectral EMG power as well as power changes of selected band ranges during clenching correlate to the extent of chewing forces.

  11. Synthesis, photodynamic activity, and quantitative structure-activity relationship modelling of a series of BODIPYs.

    Science.gov (United States)

    Caruso, Enrico; Gariboldi, Marzia; Sangion, Alessandro; Gramatica, Paola; Banfi, Stefano

    2017-02-01

    Here we report the synthesis of eleven new BODIPYs (14-24) characterized by the presence of an aromatic ring on the 8 (meso) position and of iodine atoms on the pyrrolic 2,6 positions. These molecules, together with twelve BODIPYs already reported by us (1-12), represent a large panel of BODIPYs showing different atoms or groups as substituent of the aromatic moiety. Two physico-chemical features ((1)O2 generation rate and lipophilicity), which can play a fundamental role in the outcome as photosensitizers, have been studied. The in vitro photo-induced cell-killing efficacy of 23 PSs was studied on the SKOV3 cell line treating the cells for 24h in the dark then irradiating for 2h with a green LED device (fluence 25.2J/cm(2)). The cell-killing efficacy was assessed with the MTT test and compared with that one of meso un-substituted compound (13). In order to understand the possible effect of the substituents, a predictive quantitative structure-activity relationship (QSAR) regression model, based on theoretical holistic molecular descriptors, was developed. The results clearly indicate that the presence of an aromatic ring is fundamental for an excellent photodynamic response, whereas the electronic effects and the position of the substituents on the aromatic ring do not influence the photodynamic efficacy. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

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

    2010-09-01

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

  13. Estimating active transportation behaviors to support health impact assessment in the United States

    Directory of Open Access Journals (Sweden)

    Theodore J Mansfield

    2016-05-01

    Full Text Available 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, 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 minutes 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

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

    Science.gov (United States)

    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

  15. Quantitative precipitation estimation based on high-resolution numerical weather prediction and data assimilation with WRF – a performance test

    Directory of Open Access Journals (Sweden)

    Hans-Stefan Bauer

    2015-04-01

    Full Text Available Quantitative precipitation estimation and forecasting (QPE and QPF are among the most challenging tasks in atmospheric sciences. In this work, QPE based on numerical modelling and data assimilation is investigated. Key components are the Weather Research and Forecasting (WRF model in combination with its 3D variational assimilation scheme, applied on the convection-permitting scale with sophisticated model physics over central Europe. The system is operated in a 1-hour rapid update cycle and processes a large set of in situ observations, data from French radar systems, the European GPS network and satellite sensors. Additionally, a free forecast driven by the ECMWF operational analysis is included as a reference run representing current operational precipitation forecasting. The verification is done both qualitatively and quantitatively by comparisons of reflectivity, accumulated precipitation fields and derived verification scores for a complex synoptic situation that developed on 26 and 27 September 2012. The investigation shows that even the downscaling from ECMWF represents the synoptic situation reasonably well. However, significant improvements are seen in the results of the WRF QPE setup, especially when the French radar data are assimilated. The frontal structure is more defined and the timing of the frontal movement is improved compared with observations. Even mesoscale band-like precipitation structures on the rear side of the cold front are reproduced, as seen by radar. The improvement in performance is also confirmed by a quantitative comparison of the 24-hourly accumulated precipitation over Germany. The mean correlation of the model simulations with observations improved from 0.2 in the downscaling experiment and 0.29 in the assimilation experiment without radar data to 0.56 in the WRF QPE experiment including the assimilation of French radar data.

  16. First quantitative bias estimates for tropospheric NO2 columns retrieved from SCIAMACHY, OMI, and GOME-2 using a common standard

    Directory of Open Access Journals (Sweden)

    X. Pan

    2012-06-01

    Full Text Available For the intercomparison of tropospheric nitrogen dioxide NO2 vertical column density (VCD data from three different satellite sensors (SCIAMACHY, OMI, and GOME-2, we use a common standard to quantitatively evaluate the biases for the respective data sets. As the standard, a regression analysis using a single set of collocated ground-based Multi-Axis Differential Optical Absorption Spectroscopy (MAX-DOAS observations at several sites in Japan and China in 2006–2011 is adopted. Examination of various spatial coincidence criteria indicates that the slope of the regression line can be influenced by the spatial distribution of NO2 over the area considered. While the slope varies systematically with the distance between the MAX-DOAS and satellite observation points around Tokyo in Japan, such a systematic dependence is not clearly seen and correlation coefficients are generally higher in comparisons at sites in China. On the basis of these results, we focus mainly on comparisons over China and best estimate the biases in SCIAMACHY, OMI, and GOME-2 data (TM4NO2A and DOMINO version 2 products against the MAX-DOAS observations to be −5±14 %, −10±14 %, and +1±14 %, respectively, which are all small and insignificant. We suggest that these small biases now allow analyses combining these satellite data for air quality studies that are more systematic and quantitative than previously possible.

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

    Science.gov (United States)

    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.

  18. A reliable and accurate portable device for rapid quantitative estimation of iodine content in different types of edible salt

    Directory of Open Access Journals (Sweden)

    Kapil Yadav

    2015-01-01

    Full Text Available Background: Continuous monitoring of salt iodization to ensure the success of the Universal Salt Iodization (USI program can be significantly strengthened by the use of a simple, safe, and rapid method of salt iodine estimation. This study assessed the validity of a new portable device, iCheck Iodine developed by the BioAnalyt GmbH to estimate the iodine content in salt. Materials and Methods: Validation of the device was conducted in the laboratory of the South Asia regional office of the International Council for Control of Iodine Deficiency Disorders (ICCIDD. The validity of the device was assessed using device specific indicators, comparison of iCheck Iodine device with the iodometric titration, and comparison between iodine estimation using 1 g and 10 g salt by iCheck Iodine using 116 salt samples procured from various small-, medium-, and large-scale salt processors across India. Results: The intra- and interassay imprecision for 10 parts per million (ppm, 30 ppm, and 50 ppm concentrations of iodized salt were 2.8%, 6.1%, and 3.1%, and 2.4%, 2.2%, and 2.1%, respectively. Interoperator imprecision was 6.2%, 6.3%, and 4.6% for the salt with iodine concentrations of 10 ppm, 30 ppm, and 50 ppm respectively. The correlation coefficient between measurements by the two methods was 0.934 and the correlation coefficient between measurements using 1 g of iodized salt and 10 g of iodized salt by the iCheck Iodine device was 0.983. Conclusions: The iCheck Iodine device is reliable and provides a valid method for the quantitative estimation of the iodine content of iodized salt fortified with potassium iodate in the field setting and in different types of salt.

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

    Science.gov (United States)

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

    2015-12-01

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

  20. Modified DTW for a quantitative estimation of the similarity between rainfall time series

    Science.gov (United States)

    Djallel Dilmi, Mohamed; Barthès, Laurent; Mallet, Cécile; Chazottes, Aymeric

    2017-04-01

    The Precipitations are due to complex meteorological phenomenon and can be described as intermittent process. The spatial and temporal variability of this phenomenon is significant and covers large scales. To analyze and model this variability and / or structure, several studies use a network of rain gauges providing several time series of precipitation measurements. To compare these different time series, the authors compute for each time series some parameters (PDF, rain peak intensity, occurrence, amount, duration, intensity …). However, and despite the calculation of these parameters, the comparison of the parameters between two series of measurements remains qualitative. Due to the advection processes, when different sensors of an observation network measure precipitation time series identical in terms of intermitency or intensities, there is a time lag between the different measured series. Analyzing and extracting relevant information on physical phenomena from these precipitation time series implies the development of automatic analytical methods capable of comparing two time series of precipitation measured by different sensors or at two different locations and thus quantifying the difference / similarity. The limits of the Euclidean distance to measure the similarity between the time series of precipitation have been well demonstrated and explained (eg the Euclidian distance is indeed very sensitive to the effects of phase shift : between two identical but slightly shifted time series, this distance is not negligible). To quantify and analysis these time lag, the correlation functions are well established, normalized and commonly used to measure the spatial dependences that are required by many applications. However, authors generally observed that there is always a considerable scatter of the inter-rain gauge correlation coefficients obtained from the individual pairs of rain gauges. Because of a substantial dispersion of estimated time lag, the

  1. Stereological estimation of nuclear volume and other quantitative histopathological parameters in the prognostic evaluation of supraglottic laryngeal squamous cell carcinoma

    DEFF Research Database (Denmark)

    Sørensen, Flemming Brandt; Bennedbaek, O; Pilgaard, J;

    1989-01-01

    observers of the latter was poor in the material which consisted of 35 biopsy specimens. Unbiased estimates of nuclear Vv were on the average 385 microns3 (CV = 0.44), with more than 90% of the associated variance attributable to differences in nuclear Vv among individual lesions. Nuclear Vv was positively......The aim of this study was to investigate various approaches to the grading of malignancy in pre-treatment biopsies from patients with supraglottic laryngeal squamous cell carcinoma. The prospects of objective malignancy grading based on stereological estimation of the volume-weighted mean nuclear...... volume, nuclear Vv, and nuclear volume fraction, Vv(nuc/tis), along with morphometrical 2-dimensional estimation of nuclear density index, NI, and mitotic activity index, MI, were investigated and compared with the current morphological, multifactorial grading system. The reproducibility among two...

  2. Estimation of geomagnetic activity using measure of anomalousness

    Directory of Open Access Journals (Sweden)

    Anatoly Soloviev

    2017-01-01

    Full Text Available Herein, we present a newly developed indicator for estimating geomagnetic activity. It is based on the magnitude of measure of anomalousness (MA of magnetometer recordings at a given time or interval. It is intended for automated estimation of geomagnetic activity level in the area of a specific magnetic station or in a given region using data of a set of stations. It reflects geomagnetic activity level at different observatories in a single scale [-1, 1], regardless of their latitudinal location and consequently typical disturbance amplitudes. To a certain extent MA indicator is an analog of traditional K index. However, a well-known shortcoming of the latter is its long, 3-hour update rate. Moreover, K index calculation requires subtraction of Sq variation that also causes delays. At the same time there is a demand for operational geomagnetic indices that have maximal time resolution and are available in near real-time. The proposed MA indicator aims to address the shortcomings of the traditional K index. The MA calculation may be implemented automatically with the same time resolution as the initial data are recorded.

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

    Science.gov (United States)

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

    2013-02-01

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

  4. Quantitative data for care of patients with systemic lupus erythematosus in usual clinical settings: a patient Multidimensional Health Assessment Questionnaire and physician estimate of noninflammatory symptoms.

    Science.gov (United States)

    Askanase, Anca Dinu; Castrejón, Isabel; Pincus, Theodore

    2011-07-01

    To analyze quantitative data in patients with systemic lupus erythematosus (SLE), seen in usual care, from a patient Multidimensional Health Assessment Questionnaire (MDHAQ) with routine assessment of patient index data (RAPID3) scores and from a physician global estimate of noninflammatory symptoms; and to compare results to self-report Systemic Lupus Activity Questionnaire (SLAQ) scores and 4 SLE indices: SLE Disease Activity Index-2K (SLEDAI-2K), British Isles Lupus Assessment Group (BILAG), Systemic Lupus Activity Measure (SLAM), and European Consensus Lupus Activity Measurement (ECLAM). Fifty consecutive patients with SLE were studied in usual care of one rheumatologist. All patients completed an MDHAQ/RAPID3 in this setting. Each patient also completed a SLAQ. The rheumatologist scored SLEDAI-2K, BILAG, SLAM, ECLAM, and 2 physician global estimates, one for overall status and one for noninflammatory symptoms. Patients were classified into 2 groups: "few" or "many" noninflammatory symptoms. Scores and indices were compared using correlations, cross-tabulations and t tests. The patients included 45 women and 5 men. MDHAQ/RAPID3 and SLAQ scores were significantly correlated. RAPID3 scores were significantly higher in patients with SLE index scores above median levels, and in 34 patients scored by the rheumatologist as having "few" noninflammatory symptoms. MDHAQ/RAPID3 and SLAQ were significantly higher in 16 patients scored as having many noninflammatory symptoms. MDHAQ/RAPID3 and SLAQ subscale scores appear to reflect disease activity in patients with SLE, but not in patients with many noninflammatory symptoms. A physician scale for noninflammatory symptoms is useful to interpret MDHAQ/RAPID3, SLAQ, and SLE index scores.

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

    Science.gov (United States)

    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.

  6. Design of cinnamaldehyde amino acid Schiff base compounds based on the quantitative structure–activity relationship

    Science.gov (United States)

    Hui Wang; Mingyue Jiang; Shujun Li; Chung-Yun Hse; Chunde Jin; Fangli Sun; Zhuo Li

    2017-01-01

    Cinnamaldehyde amino acid Schiff base (CAAS) is a new class of safe, bioactive compounds which could be developed as potential antifungal agents for fungal infections. To design new cinnamaldehyde amino acid Schiff base compounds with high bioactivity, the quantitative structure–activity relationships (QSARs) for CAAS compounds against Aspergillus niger (A. niger) and...

  7. 76 FR 27384 - Agency Information Collection Activity (Veteran Suicide Prevention Online Quantitative Surveys...

    Science.gov (United States)

    2011-05-11

    ... better understand Veterans and their families' awareness of VA's suicide prevention and mental health... AFFAIRS Agency Information Collection Activity (Veteran Suicide Prevention Online Quantitative Surveys.... Veterans Online Survey, VA Form 10-0513. b. Veterans Family Online Survey, VA Form 10-0513a. c....

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

    Directory of Open Access Journals (Sweden)

    Wenchao Zhang

    2016-05-01

    Full Text Available 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/.

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

    Science.gov (United States)

    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/.

  10. Non-response bias in physical activity trend estimates

    Directory of Open Access Journals (Sweden)

    Bauman Adrian

    2009-11-01

    Full Text Available Abstract Background Increases in reported leisure time physical activity (PA and obesity have been observed in several countries. One hypothesis for these apparently contradictory trends is differential bias in estimates over time. The purpose of this short report is to examine the potential impact of changes in response rates over time on the prevalence of adequate PA in Canadian adults. Methods Participants were recruited in representative national telephone surveys of PA from 1995-2007. Differences in PA prevalence estimates between participants and those hard to reach were assessed using Student's t tests adjusted for multiple comparisons. Results The number of telephone calls required to reach and speak with someone in the household increased over time, as did the percentage of selected participants who initially refused during the first interview attempt. A higher prevalence of adequate PA was observed with 5-9 attempts to reach anyone in the household in 1999-2002, but this was not significant after adjustment for multiple comparisons. Conclusion No significant impact on PA trend estimates was observed due to differential non response rates. It is important for health policy makers to understand potential biases and how these may affect secular trends in all aspects of the energy balance equation.

  11. Quantitative description of induced seismic activity before and after the 2011 Tohoku-Oki earthquake by nonstationary ETAS models

    Science.gov (United States)

    Kumazawa, Takao; Ogata, Yosihiko

    2013-12-01

    The epidemic-type aftershock sequence (ETAS) model is extended for application to nonstationary seismic activity, including transient swarm activity or seismicity anomalies, in a seismogenic region. The time-dependent rates of both background seismicity and aftershock productivity in the ETAS model are optimally estimated from hypocenter data. These rates can provide quantitative evidence for abrupt or gradual changes in shear stress and/or fault strength due to aseismic transient causes such as triggering by remote earthquakes, slow slips, or fluid intrusions within the region. This extended model is applied to data sets from several seismic events including swarms that were induced by the M9.0 Tohoku-Oki earthquake of 2011.

  12. Quantitative Structure – Antioxidant Activity Relationships of Flavonoid Compounds

    Directory of Open Access Journals (Sweden)

    Károly Héberger

    2004-12-01

    Full Text Available A quantitative structure – antioxidant activity relationship (QSAR study of 36 flavonoids was performed using the partial least squares projection of latent structures (PLS method. The chemical structures of the flavonoids have been characterized by constitutional descriptors, two-dimensional topological and connectivity indices. Our PLS model gave a proper description and a suitable prediction of the antioxidant activities of a diverse set of flavonoids having clustering tendency.

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

    National Research Council Canada - National Science Library

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

    2009-01-01

    ... 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...

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

    Science.gov (United States)

    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.

  15. Improved accuracy of quantitative parameter estimates in dynamic contrast-enhanced CT study with low temporal resolution

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sun Mo, E-mail: Sunmo.Kim@rmp.uhn.on.ca [Radiation Medicine Program, Princess Margaret Hospital/University Health Network, Toronto, Ontario M5G 2M9 (Canada); Haider, Masoom A. [Department of Medical Imaging, Sunnybrook Health Sciences Centre, Toronto, Ontario M4N 3M5, Canada and Department of Medical Imaging, University of Toronto, Toronto, Ontario M5G 2M9 (Canada); Jaffray, David A. [Radiation Medicine Program, Princess Margaret Hospital/University Health Network, Toronto, Ontario M5G 2M9, Canada and Department of Radiation Oncology, University of Toronto, Toronto, Ontario M5G 2M9 (Canada); Yeung, Ivan W. T. [Radiation Medicine Program, Princess Margaret Hospital/University Health Network, Toronto, Ontario M5G 2M9 (Canada); Department of Medical Physics, Stronach Regional Cancer Centre, Southlake Regional Health Centre, Newmarket, Ontario L3Y 2P9 (Canada); Department of Radiation Oncology, University of Toronto, Toronto, Ontario M5G 2M9 (Canada)

    2016-01-15

    quantitative histogram parameters of volume transfer constant [standard deviation (SD), 98th percentile, and range], rate constant (SD), blood volume fraction (mean, SD, 98th percentile, and range), and blood flow (mean, SD, median, 98th percentile, and range) for sampling intervals between 10 and 15 s. Conclusions: The proposed method of PCA filtering combined with the AIF estimation technique allows low frequency scanning for DCE-CT study to reduce patient radiation dose. The results indicate that the method is useful in pixel-by-pixel kinetic analysis of DCE-CT data for patients with cervical cancer.

  16. Quantitative imaging test approval and biomarker qualification: interrelated but distinct activities.

    Science.gov (United States)

    Buckler, Andrew J; Bresolin, Linda; Dunnick, N Reed; Sullivan, Daniel C; Aerts, Hugo J W L; Bendriem, Bernard; Bendtsen, Claus; Boellaard, Ronald; Boone, John M; Cole, Patricia E; Conklin, James J; Dorfman, Gary S; Douglas, Pamela S; Eidsaunet, Willy; Elsinger, Cathy; Frank, Richard A; Gatsonis, Constantine; Giger, Maryellen L; Gupta, Sandeep N; Gustafson, David; Hoekstra, Otto S; Jackson, Edward F; Karam, Lisa; Kelloff, Gary J; Kinahan, Paul E; McLennan, Geoffrey; Miller, Colin G; Mozley, P David; Muller, Keith E; Patt, Rick; Raunig, David; Rosen, Mark; Rupani, Haren; Schwartz, Lawrence H; Siegel, Barry A; Sorensen, A Gregory; Wahl, Richard L; Waterton, John C; Wolf, Walter; Zahlmann, Gudrun; Zimmerman, Brian

    2011-06-01

    Quantitative imaging biomarkers could speed the development of new treatments for unmet medical needs and improve routine clinical care. However, it is not clear how the various regulatory and nonregulatory (eg, reimbursement) processes (often referred to as pathways) relate, nor is it clear which data need to be collected to support these different pathways most efficiently, given the time- and cost-intensive nature of doing so. The purpose of this article is to describe current thinking regarding these pathways emerging from diverse stakeholders interested and active in the definition, validation, and qualification of quantitative imaging biomarkers and to propose processes to facilitate the development and use of quantitative imaging biomarkers. A flexible framework is described that may be adapted for each imaging application, providing mechanisms that can be used to develop, assess, and evaluate relevant biomarkers. From this framework, processes can be mapped that would be applicable to both imaging product development and to quantitative imaging biomarker development aimed at increasing the effectiveness and availability of quantitative imaging. http://radiology.rsna.org/lookup/suppl/doi:10.1148/radiol.10100800/-/DC1. RSNA, 2011

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

    Science.gov (United States)

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

    2015-02-21

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

  18. Physical Activity in Vietnam: Estimates and Measurement Issues.

    Directory of Open Access Journals (Sweden)

    Tan Van Bui

    Full Text Available Our aims were to provide the first national estimates of physical activity (PA for Vietnam, and to investigate issues affecting their accuracy.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.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.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.

  19. Mesoscale and Local Scale Evaluations of Quantitative Precipitation Estimates by Weather Radar Products during a Heavy Rainfall Event

    Directory of Open Access Journals (Sweden)

    Basile Pauthier

    2016-01-01

    Full Text Available A 24-hour heavy rainfall event occurred in northeastern France from November 3 to 4, 2014. The accuracy of the quantitative precipitation estimation (QPE by PANTHERE and ANTILOPE radar-based gridded products during this particular event, is examined at both mesoscale and local scale, in comparison with two reference rain-gauge networks. Mesoscale accuracy was assessed for the total rainfall accumulated during the 24-hour event, using the Météo France operational rain-gauge network. Local scale accuracy was assessed for both total event rainfall and hourly rainfall accumulations, using the recently developed HydraVitis high-resolution rain gauge network Evaluation shows that (1 PANTHERE radar-based QPE underestimates rainfall fields at mesoscale and local scale; (2 both PANTHERE and ANTILOPE successfully reproduced the spatial variability of rainfall at local scale; (3 PANTHERE underestimates can be significantly improved at local scale by merging these data with rain gauge data interpolation (i.e., ANTILOPE. This study provides a preliminary evaluation of radar-based QPE at local scale, suggesting that merged products are invaluable for applications at very high resolution. The results obtained underline the importance of using high-density rain-gauge networks to obtain information at high spatial and temporal resolution, for better understanding of local rainfall variation, to calibrate remotely sensed rainfall products.

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

    Science.gov (United States)

    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. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. A quantitative estimate on the heat transfer in cylindrical fuel rods to account for flux depression inside fuel

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Mario A.B. da; Narain, Rajendra; Vasconcelos, Wagner E. de, E-mail: narain@ufpe.b, E-mail: wagner@ufpe.b [Universidade Federal de Pernambuco (DEN/UFPE), Recife, PE (Brazil). Centro de Tecnologia e Geociencias. Dept. de Energia Nuclear

    2011-07-01

    In a nuclear reactor, the amount of power generation is limited by thermal rather than by nuclear considerations. The reactor core must be operated at a power level that the temperatures of the fuel and cladding anywhere in the core must not exceed safe limits so as to prevent from fuel element damages. Heat transfer from fuel pins can be calculated analytically by using a flat power density in the fuel pin. In actual practice, the neutron flux distribution inside fuel pins results in a smaller effective distance for the heat to be transported to the coolant. This inherent phenomenon gives rise to a heat transfer benefit in fuel pin temperatures. In this research, a quantitative estimate for transferring heat from cylindrical fuel rods is accomplished by considering a non-uniform neutron flux, which leads to a flux depression factor. This, in turn, shifts the temperature inside the fuel pin. A theoretical relationship combining the flux depression factor and a ratio of temperature gradients for uniform and non-uniform is derived, and a computational program, based on energy balance, is developed to validate the considered approximation. (author)

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

    Science.gov (United States)

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

    2008-07-01

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

  3. Quantitative structure activity relationship study of anticonvulsant activity of α_substituted acetamido-N-benzylacetamide derivatives

    Directory of Open Access Journals (Sweden)

    Usman Abdulfatai

    2016-12-01

    Full Text Available To develop the quantitative structure–activity relationship (QSAR for predicting the anticonvulsant activity of α_substituted acetamido-N-benzylacetamide derivatives. Density Functional Theory (B3LYP/6-31G* quantum chemical calculation method was used to find the optimized geometry of the studied molecules. Nine types of molecular descriptors were used to derive a quantitative relation between anticonvulsant activity and structural properties. The relevant molecular descriptors were selected by genetic algorithm approximation. The high value of the correlation coefficient, (R2 of 0.98, indicates that the model was satisfactory. The proposed model has good stability, robustness, and predictability on verifying with internal and external validation.

  4. Cyclotide structure-activity relationships: qualitative and quantitative approaches linking cytotoxic and anthelmintic activity to the clustering of physicochemical forces.

    Directory of Open Access Journals (Sweden)

    Sungkyu Park

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

  5. Calculation of Quantitative Structure-Activity Relationship Descriptors of Artemisinin Derivatives

    Directory of Open Access Journals (Sweden)

    Jambalsuren Bayarmaa

    2008-06-01

    Full Text Available Quantitative structure-activity relationships are based on the construction of predictive models using a set of known molecules and associated activity value. This accurate methodology, developed with adequate mathematical and computational tools, leads to a faster, cheaper and more comprehensive design of new products, reducing the experimental synthesis and testing on animals. Preparation of the QSAR models of artemisinin derivatives was carried out by the genetic function algorithm (GFA method for 91 molecules. The results show some relationships to the observed antimalarial activities of the artemisinin derivatives. The most statistically signi fi cant regression equation obtained from the fi nal GFA relates to two molecular descriptors.

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

    Science.gov (United States)

    Knight, J L; Weaver, D F

    1998-10-01

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

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

    Directory of Open Access Journals (Sweden)

    P. Jaiswal

    2011-06-01

    Full Text Available 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

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

    Science.gov (United States)

    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

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

    OpenAIRE

    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 r...

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

    OpenAIRE

    Jing eWang; Juan eLiu; Ming eKang

    2015-01-01

    Flow cytometry (FCM) is a commonly used method for estimating genome size in many organisms. The use of flow cytometry 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...

  11. Quantitative Measurement of Physical Activity in Acute Ischemic Stroke and Transient Ischemic Attack

    DEFF Research Database (Denmark)

    Strømmen, Anna Maria; Christensen, Thomas; Jensen, Kai

    2014-01-01

    BACKGROUND AND PURPOSE: The purpose of this study was to quantitatively measure and describe the amount and pattern of physical activity in patients within the first week after acute ischemic stroke and transient ischemic attack using accelerometers. METHODS: A total of 100 patients with acute is...... ischemic stroke. The method offers a low cost and noninvasive tool for future clinical interventional physiotherapeutic and early mobilization studies. CLINICAL TRIAL REGISTRATION: URL: http://www.clinicaltrials.gov. Unique identifier: NCT01560520....

  12. Estimation of coronary artery stenosis by low-dose adenosine stress real-time myocardial contrast echocardiography: a quantitative study

    Institute of Scientific and Technical Information of China (English)

    ZHOU Xiao; ZHI Guang; XU Yong; WANG Jing; YAN Guo-hui

    2012-01-01

    Background Coronary microcirculation reserve is an important field in the research of coronary artery disease,but it is difficult to identify clinically.Currently it is widely accepted that myocardial contrast echocardiography (MCE) is a safe,inexpensive method and has comparatively high image resolution.The present study used quantitative low-dose adenosine stress real-time (RT)-MCE to estimate myocardial perfusion and the coronary stenosis.Methods Forty-nine left ventricular (LV) segments from 14 unselected patients were divided into three groups according to the coronary angiography or CT angiography results:group 1 (n=20,41%) without significant stenosis (<70%),group 2 (n=12,24%)with successful percutaneous coronary intervention (PCI),and group 3 (n=17,35%)with significant stenosis (>70%).RT-MCE was performed in these patients with low-dose adenosine stress and continuous infusion of Sonovue.The replenishing curves were drawn according to the contrast density measured at the end-diastolic frame of every cardiac circle by ACQ software.Results Forty-nine LV segments with satisfactory image quality were picked for quantitative contrast echo analysis.The replenishing curves were analyzed at baseline and after stress.Perfusion of group 3 did not decrease significantly at baseline,and showed no improvement during adenosine stress and was significantly different from groups 1 and 2 (P <0.05).The A·β and β increased more significantly in group 1 than in groups 2 and 3 (P <0.05).In a receiver operating characteristic (ROC) curve analysis,A·β under adenosine stress <1.74 dB/s had a sensitivity and specificity of 71% for diagnosis of coronary artery stenosis,reduced adenosine-induced rise (percentage of A·β <81%) had a sensitivity and specificity of 83% and 79% for the diagnosis of low-reserve,and β <54% had a sensitivity of 86% and specificity of 79%.Conclusions Rest perfusion of severely stenosed arteries may be normal

  13. In Vivo Quantitative Measurement of Arthritis Activity Based on Hydrophobically Modified Glycol Chitosan in Inflammatory Arthritis: More Active than Passive Accumulation

    Directory of Open Access Journals (Sweden)

    Kyeong Soon Park

    2012-09-01

    Full Text Available We demonstrated that arthritis could be visualized noninvasively using hydrophobically modified glycol chitosan nanoparticles labeled with Cy5.5 (HGC-Cy5.5 and an optical imaging system. Activated macrophages expressing Mac-1 molecules effectively phagocytosed HGC-Cy5.5, which formed spherical nanoparticles under physiologic conditions. We estimated the applicability of HGC-Cy5.5 to quantitative analysis of arthritis development and progression. Near-infrared fluorescence images, captured after HGC-Cy5.5 injection in mice with collagen-induced arthritis, showed stronger fluorescence intensity in the active arthritis group than in the nonarthritis group. According to the progression of arthritis in both collagen-induced arthritis and collagen antibody-induced arthritis models, total photon counts (TPCs increased in parallel with the clinical arthritis index. Quantitative analysis of fluorescence after treatment with methotrexate showed a significant decrease in TPC in a dose-dependent manner. Histologic evaluation confirmed that the mechanism underlying selective accumulation of HGC-Cy5.5 within synovitis tissues included enhanced phagocytosis of the probe by Mac-1-expressing macrophages as well as enhanced permeability through leaky vessels. These results suggest that optical imaging of arthritis using HGC-Cy5.5 can provide an objective measurement of disease activity and, at the same time, therapeutic responses in rheumatoid arthritis.

  14. Activated sludge characterization through microscopy: A review on quantitative image analysis and chemometric techniques

    Energy Technology Data Exchange (ETDEWEB)

    Mesquita, Daniela P. [IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga (Portugal); Amaral, A. Luís [IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga (Portugal); Instituto Politécnico de Coimbra, ISEC, DEQB, Rua Pedro Nunes, Quinta da Nora, 3030-199 Coimbra (Portugal); Ferreira, Eugénio C., E-mail: ecferreira@deb.uminho.pt [IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga (Portugal)

    2013-11-13

    Graphical abstract: -- Highlights: •Quantitative image analysis shows potential to monitor activated sludge systems. •Staining techniques increase the potential for detection of operational problems. •Chemometrics combined with quantitative image analysis is valuable for process monitoring. -- Abstract: In wastewater treatment processes, and particularly in activated sludge systems, efficiency is quite dependent on the operating conditions, and a number of problems may arise due to sludge structure and proliferation of specific microorganisms. In fact, bacterial communities and protozoa identification by microscopy inspection is already routinely employed in a considerable number of cases. Furthermore, quantitative image analysis techniques have been increasingly used throughout the years for the assessment of aggregates and filamentous bacteria properties. These procedures are able to provide an ever growing amount of data for wastewater treatment processes in which chemometric techniques can be a valuable tool. However, the determination of microbial communities’ properties remains a current challenge in spite of the great diversity of microscopy techniques applied. In this review, activated sludge characterization is discussed highlighting the aggregates structure and filamentous bacteria determination by image analysis on bright-field, phase-contrast, and fluorescence microscopy. An in-depth analysis is performed to summarize the many new findings that have been obtained, and future developments for these biological processes are further discussed.

  15. Quantitative in vivo CT arthrography of the human osteoarthritic knee to estimate cartilage sulphated glycosaminoglycan content : correlation with ex-vivo reference standards

    NARCIS (Netherlands)

    van Tiel, J; Siebelt, M; Reijman, M; Bos, P.K.; Waarsing, J H; Zuurmond, A-M; Nasserinejad, K; van Osch, G J V M; Verhaar, J A N; Krestin, G P; Weinans, H; Oei, E H G

    OBJECTIVE: Recently, computed tomography arthrography (CTa) was introduced as quantitative imaging biomarker to estimate cartilage sulphated glycosaminoglycan (sGAG) content in human cadaveric knees. Our aim was to assess the correlation between in vivo CTa in human osteoarthritis (OA) knees and ex

  16. Quantitative in vivo CT arthrography of the human osteoarthritic knee to estimate cartilage sulphated glycosaminoglycan content: correlation with ex-vivo reference standards

    NARCIS (Netherlands)

    Tiel, J. van; Siebelt, M.; Reijman, M.; Bos, P.K.; Waarsing, J.H.; Zuurmond, A.M.; Nasserinejad, K.; Osch, G.J.V.M. van; Verhaar, J.A.N.; Krestin, G.P.; Weinans, H.; Oei, E.H.G.

    2016-01-01

    Objective. Recently, computed tomography arthrography (CTa) was introduced as quantitative imaging biomarker to estimate cartilage sulphated glycosaminoglycan (sGAG) content in human cadaveric knees. Our aim was to assess the correlation between in vivo CTa in human osteoarthritis (OA) knees and ex

  17. Finding Biomass Degrading Enzymes Through an Activity-Correlated Quantitative Proteomics Platform (ACPP)

    Science.gov (United States)

    Ma, Hongyan; Delafield, Daniel G.; Wang, Zhe; You, Jianlan; Wu, Si

    2017-04-01

    The microbial secretome, known as a pool of biomass (i.e., plant-based materials) degrading enzymes, can be utilized to discover industrial enzyme candidates for biofuel production. Proteomics approaches have been applied to discover novel enzyme candidates through comparing protein expression profiles with enzyme activity of the whole secretome under different growth conditions. However, the activity measurement of each enzyme candidate is needed for confident "active" enzyme assignments, which remains to be elucidated. To address this challenge, we have developed an Activity-Correlated Quantitative Proteomics Platform (ACPP) that systematically correlates protein-level enzymatic activity patterns and protein elution profiles using a label-free quantitative proteomics approach. The ACPP optimized a high performance anion exchange separation for efficiently fractionating complex protein samples while preserving enzymatic activities. The detected enzymatic activity patterns in sequential fractions using microplate-based assays were cross-correlated with protein elution profiles using a customized pattern-matching algorithm with a correlation R-score. The ACPP has been successfully applied to the identification of two types of "active" biomass-degrading enzymes (i.e., starch hydrolysis enzymes and cellulose hydrolysis enzymes) from Aspergillus niger secretome in a multiplexed fashion. By determining protein elution profiles of 156 proteins in A. niger secretome, we confidently identified the 1,4-α-glucosidase as the major "active" starch hydrolysis enzyme (R = 0.96) and the endoglucanase as the major "active" cellulose hydrolysis enzyme (R = 0.97). The results demonstrated that the ACPP facilitated the discovery of bioactive enzymes from complex protein samples in a high-throughput, multiplexing, and untargeted fashion.

  18. Finding Biomass Degrading Enzymes Through an Activity-Correlated Quantitative Proteomics Platform (ACPP)

    Science.gov (United States)

    Ma, Hongyan; Delafield, Daniel G.; Wang, Zhe; You, Jianlan; Wu, Si

    2017-01-01

    The microbial secretome, known as a pool of biomass (i.e., plant-based materials) degrading enzymes, can be utilized to discover industrial enzyme candidates for biofuel production. Proteomics approaches have been applied to discover novel enzyme candidates through comparing protein expression profiles with enzyme activity of the whole secretome under different growth conditions. However, the activity measurement of each enzyme candidate is needed for confident "active" enzyme assignments, which remains to be elucidated. To address this challenge, we have developed an Activity-Correlated Quantitative Proteomics Platform (ACPP) that systematically correlates protein-level enzymatic activity patterns and protein elution profiles using a label-free quantitative proteomics approach. The ACPP optimized a high performance anion exchange separation for efficiently fractionating complex protein samples while preserving enzymatic activities. The detected enzymatic activity patterns in sequential fractions using microplate-based assays were cross-correlated with protein elution profiles using a customized pattern-matching algorithm with a correlation R-score. The ACPP has been successfully applied to the identification of two types of "active" biomass-degrading enzymes (i.e., starch hydrolysis enzymes and cellulose hydrolysis enzymes) from Aspergillus niger secretome in a multiplexed fashion. By determining protein elution profiles of 156 proteins in A. niger secretome, we confidently identified the 1,4-α-glucosidase as the major "active" starch hydrolysis enzyme (R = 0.96) and the endoglucanase as the major "active" cellulose hydrolysis enzyme (R = 0.97). The results demonstrated that the ACPP facilitated the discovery of bioactive enzymes from complex protein samples in a high-throughput, multiplexing, and untargeted fashion.

  19. Quantitative precipitation estimates for the northeastern Qinghai-Tibetan Plateau over the last 18,000 years

    Science.gov (United States)

    Li, Jianyong; Dodson, John; Yan, Hong; Cheng, Bo; Zhang, Xiaojian; Xu, Qinghai; Ni, Jian; Lu, Fengyan

    2017-05-01

    Quantitative information regarding the long-term variability of precipitation and vegetation during the period covering both the Late Glacial and the Holocene on the Qinghai-Tibetan Plateau (QTP) is scarce. Herein, we provide new and numerical reconstructions for annual mean precipitation (PANN) and vegetation history over the last 18,000 years using high-resolution pollen data from Lakes Dalianhai and Qinghai on the northeastern QTP. Hitherto, five calibration techniques including weighted averaging, weighted average-partial least squares regression, modern analogue technique, locally weighted weighted averaging regression, and maximum likelihood were first employed to construct robust inference models and to produce reliable PANN estimates on the QTP. The biomization method was applied for reconstructing the vegetation dynamics. The study area was dominated by steppe and characterized with a highly variable, relatively dry climate at 18,000-11,000 cal years B.P. PANN increased since the early Holocene, obtained a maximum at 8000-3000 cal years B.P. with coniferous-temperate mixed forest as the dominant biome, and thereafter declined to present. The PANN reconstructions are broadly consistent with other proxy-based paleoclimatic records from the northeastern QTP and the northern region of monsoonal China. The possible mechanisms behind the precipitation changes may be tentatively attributed to the internal feedback processes of higher latitude (e.g., North Atlantic) and lower latitude (e.g., subtropical monsoon) competing climatic regimes, which are primarily modulated by solar energy output as the external driving force. These findings may provide important insights into understanding the future Asian precipitation dynamics under the projected global warming.

  20. Telomerase Activity Detected by Quantitative Assay in Bladder Carcinoma and Exfoliated Cells in Urine

    Directory of Open Access Journals (Sweden)

    Roberta Fedriga

    2001-01-01

    Full Text Available Early diagnosis is one of the most determining factors for patient survival. The detection of telomerase activity is a potentially promising tool in the diagnosis of bladder and other types of cancer due to the high expression of this enzyme in tumor cells. We carried out a quantitative evaluation of telomerase activity in urine samples in an attempt to determine a cut-off capable of identifying cancer patients. Telomerase activity was quantified by fluorescence TRAP assay in urine from 50 healthy volunteers and in urine and bioptic tumor samples from 56 previously untreated bladder cancer patients and expressed in arbitrary enzymatic units (AEU. Telomerase activity in urine ranged from 0 to 106 AEU (median 0 in healthy donors and from 0 to 282 AEU (median 87 in patients with cancer. A telomerase expression higher than the cut off value determined by receiver operating characteristic (ROC analysis was observed in 78% of cases, regardless of tumor grade and in 71% (15/21 of cases of nonassessable or negative cytology. The quantitative analysis of telomerase activity in urine enabled us to define cut-off values characterized by different sensitivity and specificity. Cytologic and telomerase determination, used sequentially, enabled us to detect about 90% of tumors.

  1. Quantitative Metabolomics:Analysis on Active Components in Extracts from Kaki Folium

    Institute of Scientific and Technical Information of China (English)

    DAI Li-peng; GU Yuan; YIN Ren-jie; LIU Chang-xiao; SI Duan-yun

    2012-01-01

    Objective In order to analyze the active components in the extracts from Kaki Folium(KF),quantitative metabolomics approach was adopted to investigate the number of active components existing among the different extracts and their variation.Methods LC-MS method was established for the quantitative determination of the active components taking the mixture with reference substance as tested sample.Results In terms of the number of active components and amount presented in the different tested samples of KF extracted by many types of solvents,variation was observed.But rutin,astragalin,and kaempferol were presented in all samples.Difference was found between the samples extracted from the products on market and from the raw materials of KF processed by polar solvents with different recipes.However,the three active components were found in all samples examined.Conclusion These results might be valuable as all information and could be used for the optimization of raw materials extraction procedure to enhance the productivity.

  2. Quantitative measurement of speech sound distortions with the aid of minimum variance spectral estimation method for dentistry use.

    Science.gov (United States)

    Bereteu, L; Drăgănescu, G E; Stănescu, D; Sinescu, C

    2011-12-01

    In this paper, we search an adequate quantitative method based on minimum variance spectral analysis in order to reflect the dependence of the speech quality on the correct positioning of the dental prostheses. We also search some quantitative parameters, which reflect the correct position of dental prostheses in a sensitive manner.

  3. Making College Count: An Examination of Quantitative Reasoning Activities in Higher Education

    Directory of Open Access Journals (Sweden)

    Louis M. Rocconi

    2013-07-01

    Full Text Available Findings from national studies along with more frequent calls from those who employ college graduates suggest an urgent need for colleges and universities to increase opportunities for students to develop quantitative reasoning (QR skills. To address this issue, the current study examines the relationship between the frequency of QR activities during college and student and institutional characteristics, as well as whether students at institutions with an emphasis on QR (at least one QR course requirement for all students report more QR activity. Results show that gender, race-ethnicity, major, full-time status, first-generation status, age, institutional enrollment size, and institutional control are related to the frequency of QR activities. Findings also suggest that such activities are indeed more common among institutions that emphasize QR.

  4. 多QTL定位的压缩估计方法%Shrinkage Estimation Method for Mapping Multiple Quantitative Trait Loci

    Institute of Scientific and Technical Information of China (English)

    章元明

    2006-01-01

    本文综述了多标记分析和多QTL定位的压缩估计方法.对于前者,Xu(Genetics,2003,163:789-801)首先提出了Bayesian压缩估计方法.其关键在于让每个效应有一个特定的方差参数,而该方差又服从一定的先验分布,以致能从资料中估计之.由此,能够同时估计大量分子标记基因座的遗传效应,即使大多数标记的效应是可忽略的.然而,对于上位性遗传模型,其运算时间还是过长.为此,笔者将上述思想嵌入极大似然法,提出了惩罚最大似然方法.模拟研究显示:该方法能处理变量个数大于样本容量10倍左右的线性遗传模型.对于后者,本文详细介绍了基于固定区间和可变区间的Bayesian压缩估计方法.固定区间方法可处理中等密度的分子标记资料;可变区间方法则可分析高密度分子标记资料,甚至是上位性遗传模型.对于上位性检测,已介绍的惩罚最大似然方法和可变区间Bayesian压缩估计方法可供利用.应当指出,压缩估计方法在今后的eQTL和QTN定位以及基因互作网络分析等研究中也是有应用价值的.%In this article, shrinkage estimation method for multiple-marker analysis and for mapping multiple quantitative trait loci (QTL) was reviewed. For multiple-marker analysis, Xu (Genetics, 2003, 163:789-801) developed a Bayesian shrinkage estimation (BSE) method. The key to the success of this method is to allow each marker effect have its own variance parameter, which in turn has its own prior distribution so that the variance can be estimated from the data. Under this hierarchical model, a large number of markers can be handled although most of them may have negligible effects. Under epistatic genetic model, however, the running time is very long. To overcome this problem, a novel method of incorporating the idea described above into maximum likelihood,known as penalized likelihood method, was proposed. A simulated study showed that this method can

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

    Energy Technology Data Exchange (ETDEWEB)

    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

  6. Quantitative structure-activity relationship of estrogen activities of bisphenol A analogs

    Institute of Scientific and Technical Information of China (English)

    CUI Shihai; LIU Shushen; YANG Jing; WANG Xiaodong; WANG Liansheng

    2006-01-01

    The molecular electronegativity-distance vector (MEDV) is employed to describe the chemical structure of bisphenol A analogs and their correlated estrogen activities. The result shows that the constructed models have good predictability and indicates substructures that may influence estrogen activities of chemicals.

  7. A novel quantitative fluorescent reporter assay for RAG targets and RAG activity

    Directory of Open Access Journals (Sweden)

    Ines eTrancoso

    2013-05-01

    Full Text Available Recombination-Activating Genes (RAG 1 and 2 form the site specific recombinase that mediates V(DJ recombination, a process of DNA editing required for lymphocyte development and responsible for their diverse repertoire of antigen receptors. Mistargeted RAG activity associates with genome alteration and is responsible for various lymphoid tumors. Moreover several non-lymphoid tumors express RAG ectopically. A practical and powerful tool to perform quantitative assessment of RAG activity and to score putative RAG-Recognition signal sequences (RSS is required in the fields of immunology, oncology, gene therapy and development.Here we report the detailed characterization of a novel fluorescence-based reporter of RAG activity, named GFPi, a tool that allows measuring recombination efficiency by simple FACS analysis. GFPi can be produced both as a plasmid for transient transfection experiments in cell lines or as a retrovirus for stable integration in the genome, thus supporting ex vivo and in vivo studies. The GFPi assay faithfully quantified endogenous and ectopic RAG activity as tested in genetically modified fibroblasts, tumor derived cell lines, developing pre B cells and hematopoietic cells. The GFPi assay also successfully ranked the recombination efficiency of various RSS pairs, including bona fide RSS associated with V(DJ segments, artificial consensus sequences modified or not at specific nucleotides known to affect their efficiencies, or cryptic RSS involved in RAG-dependent activation of oncogenes.Our work validates the GFPi reporter as a practical quantitative tool for the study of RAG activity and RSS efficiencies. It should turn useful for the study of RAG mediated V(DJ and aberrant rearrangements, lineage commitment and vertebrate evolution.

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

    Directory of Open Access Journals (Sweden)

    Sohler Nancy L

    2009-06-01

    Full Text Available Abstract 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

  9. Improvement of Radar Quantitative Precipitation Estimation Based on Real-Time Adjustments to Z-R Relationships and Inverse Distance Weighting Correction Schemes

    Institute of Scientific and Technical Information of China (English)

    WANG Gaili; LIU Liping; DING Yuanyuan

    2012-01-01

    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 adjustnent to the Z-R relationship scheme is used to remove systematic bias on the time-domain.The gauge-corrected,radar-based,estination 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 underestination of rainfall but also reduced the root-mean-square error and the mean relative error of radar-rain gauge pairs.

  10. Quantitative MRI for Analysis of Active Multiple Sclerosis Lesions without Gadolinium-Based Contrast Agent.

    Science.gov (United States)

    Blystad, I; Håkansson, I; Tisell, A; Ernerudh, J; Smedby, Ö; Lundberg, P; Larsson, E-M

    2016-01-01

    Contrast-enhancing MS lesions are important markers of active inflammation in the diagnostic work-up of MS and in disease monitoring with MR imaging. Because intravenous contrast agents involve an expense and a potential risk of adverse events, it would be desirable to identify active lesions without using a contrast agent. The purpose of this study was to evaluate whether pre-contrast injection tissue-relaxation rates and proton density of MS lesions, by using a new quantitative MR imaging sequence, can identify active lesions. Forty-four patients with a clinical suspicion of MS were studied. MR imaging with a standard clinical MS protocol and a quantitative MR imaging sequence was performed at inclusion (baseline) and after 1 year. ROIs were placed in MS lesions, classified as nonenhancing or enhancing. Longitudinal and transverse relaxation rates, as well as proton density were obtained from the quantitative MR imaging sequence. Statistical analyses of ROI values were performed by using a mixed linear model, logistic regression, and receiver operating characteristic analysis. Enhancing lesions had a significantly (P relaxation rate (1.22 ± 0.36 versus 0.89 ± 0.24), a higher mean transverse relaxation rate (9.8 ± 2.6 versus 7.4 ± 1.9), and a lower mean proton density (77 ± 11.2 versus 90 ± 8.4) than nonenhancing lesions. An area under the receiver operating characteristic curve value of 0.832 was obtained. Contrast-enhancing MS lesions often have proton density and relaxation times that differ from those in nonenhancing lesions, with lower proton density and shorter relaxation times in enhancing lesions compared with nonenhancing lesions. © 2016 by American Journal of Neuroradiology.

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

    Institute of Scientific and Technical Information of China (English)

    Hui ZHANG; Lu ZHANG; Li-juan PENG; Xiao-wu DONG; Di WU; Vivian Chi-Hua WU; Feng-qin FENG

    2012-01-01

    Fatty acids and derivatives (FADs) are resources for natural antimicrobials.In order to screen for additional potent antimicrobial agents,the antimicrobial activities of FADs against Staphylococcus aureus were examined using a microplate assay.Monoglycerides of fatty acids were the most potent class of fatty acids,among which monotridecanoin possessed the most potent antimicrobial activity.The conventional quantitative structure-activity relationship (QSAR) and comparative molecular field analysis (CoMFA) were performed to establish two statistically reliable models (conventional QSAR:R2=0.942,Q2LOO=0.910; CoMFA:R2=0.979,Q2=0.588,respectively).Improved forecasting can be achieved by the combination of these two models that provide a good insight into the structureactivity relationships of the FADs and that may be useful to design new FADs as antimicrobial agents.

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

    Directory of Open Access Journals (Sweden)

    Fiona M. Keane

    2014-01-01

    Full Text Available 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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2016-01-01

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

  15. Quantitative structure-activity relationship studies of [(biphenyloxy)propyl]isoxazole derivatives. Inhibitors of human rhinovirus 2 replication.

    Science.gov (United States)

    Kuz'min, Victor E; Artemenko, Anatoly G; Muratov, Eugene N; Volineckaya, Ingrid L; Makarov, Vadim A; Riabova, Olga B; Wutzler, Peter; Schmidtke, Michaela

    2007-08-23

    The 50% cytotoxic concentration (CC50) in HeLa cells, the 50% inhibitory concentration (IC50) against human rhinovirus 2 (HRV-2), and the selectivity index (SI = CC50/IC50) of [(biphenyloxy)propyl]isoxazole derivatives were used to develop quantitative structure-activity relationships (QSAR) based on simplex representation of molecular structure. Statistic characteristics for partial least-squares models are quite satisfactory (R2 = 0.838 - 0.918; Q2 = 0.695 - 0.87) for prediction of CC50, IC50, and SI values and permit the virtual screening and molecular design of new compounds with strong anti-HRV-2 activity. The quality of prognosis for designed compounds was additionally estimated by analysis of domain applicability for each QSAR model. A hypothesis to the effect that terminal benzene substituents must have negative electrostatic potential and definite length (approximately 5.5-5.6 A) to possess strong antiviral activity has been suggested. The quality of developed analysis, i.e., high level of antiviral action of three new designed compounds, has been confirmed experimentally.

  16. Estimation of saturation activities for activation experiments in CHARM and CSBF using Fluence Conversion Coefficients

    CERN Document Server

    Guerin, Helene Chloe; Iliopoulou, Elpida; CERN. Geneva. HSE Department

    2017-01-01

    As summer student at CERN, I have been working in the Radiation Protection group for 10 weeks. I worked with the \\textsc{Fluka} Monte Carlo simulation code, using Fluence Conversion Coefficients method to perform simulations to estimate the saturation activities for activation experiments in the \\textsc{CSBF} and the \\textsc{Charm} facility in the East Experimental Area. The provided results will be used to plan a Monte Carlo benchmark in the \\textsc{CSBF} during a beam period at the end of August 2017.

  17. Line Impedance Estimation Using Active and Reactive Power Variations

    DEFF Research Database (Denmark)

    Timbus, Adrian Vasile; Rodriguez, Pedro; Teodorescu, Remus;

    2007-01-01

    This paper proposes an estimation method of power system impedance based on power variations caused by a distributed power generation system (DPGS) at the point of common coupling (PCC). The proposed algorithm is computationally simple and uses the voltage variations at the point of common coupling...... (PCC) caused by the variations of the power delivered to utility network to derive the value of grid impedance. Accurate estimation of both resistive and inductive part of the impedance is obtained, as the results presented show....

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

    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. Copyright © 2013 Elsevier B.V. All rights reserved.

  20. Estimation of the measurement uncertainty in quantitative determination of ketamine and norketamine in urine using a one-point calibration method.

    Science.gov (United States)

    Ma, Yi-Chun; Wang, Che-Wei; Hung, Sih-Hua; Chang, Yan-Zin; Liu, Chia-Reiy; Her, Guor-Rong

    2012-09-01

    An approach was proposed for the estimation of measurement uncertainty for analytical methods based on one-point calibration. The proposed approach is similar to the popular multiple-point calibration approach. However, the standard deviation of calibration was estimated externally. The approach was applied to the estimation of measurement uncertainty for the quantitative determination of ketamine (K) and norketamine (NK) at a 100 ng/mL threshold concentration in urine. In addition to uncertainty due to calibration, sample analysis was the other major source of uncertainty. To include the variation due to matrix effect and temporal effect in sample analysis, different blank urines were spiked with K and NK and analyzed at equal time intervals within and between batches. The expanded uncertainties (k = 2) were estimated to be 10 and 8 ng/mL for K and NK, respectively.

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

    Directory of Open Access Journals (Sweden)

    D. Anghileri

    2011-01-01

    Full Text Available 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.

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

    Directory of Open Access Journals (Sweden)

    D. Anghileri

    2011-06-01

    Full Text Available 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.

  3. 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.

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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...

  5. Estimation methods and monitoring network issues in the quantitative estimation of land-based COD and TN loads entering the sea: a case study in Qingdao City, China.

    Science.gov (United States)

    Su, Ying; Wang, Xiulin; Li, Keqiang; Liang, Shengkang; Qian, Guodong; Jin, Hong; Dai, Aiquan

    2014-09-01

    At present, the monitoring network of China cannot provide sufficient data to estimate land-based pollutant loads that enter the sea, and estimation methods are imprecisely used. In this study, the selection of monitoring stations, monitoring frequency, and pollutant load estimation methods was studied in Qingdao City, a typical coastal city in China, taken as an example. Land-based pollutant loads from Qingdao were estimated, and load distribution, density, and composition were analyzed to identify the key pollution source regions (SRs) that need to be monitored and controlled. Results show that the administrative land area of Qingdao can be divided into 25 sea-sink source regions (SSRs). A total of 14 more rivers and 62 industrial enterprises should be monitored to determine the comprehensive pollutant loads of the city. Furthermore, the monitoring frequency of rivers should not be less than three times/year; a monitoring frequency of five or more times is preferable. The findings on pollutant load estimation with the use of different estimation methods substantially vary; estimation results with the use of ratio-based methods were 10 and 22 % higher than those with the use of monitoring-based methods in terms of chemical oxygen demand (COD) and total nitrogen (TN), respectively. None-point sources contributed the majority of the pollutant loads at about 70 % of the total COD and 60 % of the total TN.

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

    Science.gov (United States)

    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.

  7. QUANTITATIVE ELECTRONIC STRUCTURE - ACTIVITY RELATIONSHIPS ANALYSIS ANTIMUTAGENIC BENZALACETONE DERIVATIVES BY PRINCIPAL COMPONENT REGRESSION APPROACH

    Directory of Open Access Journals (Sweden)

    Yuliana Yuliana

    2010-06-01

    Full Text Available Quantitative Electronic Structure Activity Relationship (QSAR analysis of a series of benzalacetones has been investigated based on semi empirical PM3 calculation data using Principal Components Regression (PCR. Investigation has been done based on antimutagen activity from benzalacetone compounds (presented by log 1/IC50 and was studied as linear correlation with latent variables (Tx resulted from transformation of atomic net charges using Principal Component Analysis (PCA. QSAR equation was determinated based on distribution of selected components and then was analysed with PCR. The result was described by the following QSAR equation : log 1/IC50 = 6.555 + (2.177.T1 + (2.284.T2 + (1.933.T3 The equation was significant on the 95% level with statistical parameters : n = 28 r = 0.766  SE  = 0.245  Fcalculation/Ftable = 3.780 and gave the PRESS result 0.002. It means that there were only a relatively few deviations between the experimental and theoretical data of antimutagenic activity.          New types of benzalacetone derivative compounds were designed  and their theoretical activity were predicted based on the best QSAR equation. It was found that compounds number 29, 30, 31, 32, 33, 35, 36, 37, 38, 40, 41, 42, 44, 47, 48, 49 and 50  have  a relatively high antimutagenic activity.   Keywords: QSAR; antimutagenic activity; benzalaceton; atomic net charge

  8. Quantitative structure-activity relationships for the Toxicity of Substituted Benzenes to Cyprinus carpio

    Institute of Scientific and Technical Information of China (English)

    GUANG-HUA LU; CHAO WANG; XING YUAN; PEI-ZHEN LAN

    2005-01-01

    Objective To measure the 96h-LC50 values of 32 substituted benzenes to the carp and to study the relationship between quantitative structure-activity and structural parameters of chemicals. Methods The acute toxicity values of 32 substituted benzenes to the carp were determined in a semistatic test. The energy of the lowest unoccupied molecular orbital, and the highest occupied molecular orbital, the dipole moment and the molecular weight of substituted benzenes were calculated by the quantum chemical method MOPAC6.0. Results The range of the toxicity of studied compounds was broad, and the most toxic compound was pentachlorophenol, while the least toxic compound was 4-methylaniline. By the stepwise regression analyses, a series of Quantitative structure-activity relationships (QSAR) equations were derived from all compounds and subclasses. The equation log1/LC50=0.759logP +2.222 (R2 (adj)=0.818) was found to fit well and the average predicted percentage error was 6.16%. Conclusion The toxicity of anilines and phenols to the carp could be modeled well by logP alone, whereas the toxicity of the halogenated benzenes and nitrobenznes not containing hydroxyl or amino group can be controlled by hydrophobic and electronic factors.

  9. Qualitative and quantitative measurement of human brain activity using pixel subtraction algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jin Myoung; Jeong, Gwang Woo; Kim, Hyung Joong; Cho, Seong Hoon; Kang, Heoung Keun; Seo, Jeong Jin; Park, Seung Jin [School of Medicine, Chonnam National Univ., Kwangju (Korea, Republic of)

    2004-08-01

    manual quantification method showed an average error of 0.334{+-}0.007 (%). Thus, the manual counting method gave less accurate quantitative information on brain activation than the FALBA program. The FALBA program is capable of providing accurate quantitative results, including the identification of the brain activation region and lateralization index with respect to the functional and anatomical areas. Also, the processing time was dramatically shortened in comparison with the manual counting method.

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

    Science.gov (United States)

    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.

  11. Quantitative structure-activity relationships of selective antagonists of glucagon receptor using QuaSAR descriptors.

    Science.gov (United States)

    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.

  12. A Quantitative High-Throughput Screening Data Analysis Pipeline for Activity Profiling.

    Science.gov (United States)

    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.

  13. Quantitative Structure Activity Relationship of Cinnamaldehyde Compounds against Wood-Decaying Fungi

    Directory of Open Access Journals (Sweden)

    Dongmei Yang

    2016-11-01

    Full Text Available Cinnamaldehyde, of the genius Cinnamomum, is a major constituent of the bark of the cinnamon tree and possesses broad-spectrum antimicrobial activity. In this study, we used best multiple linear regression (BMLR to develop quantitative structure activity relationship (QSAR models for cinnamaldehyde derivatives against wood-decaying fungi Trametes versicolor and Gloeophyllun trabeum. Based on the two optimal QSAR models, we then designed and synthesized two novel cinnamaldehyde compounds. The QSAR models exhibited good correlation coefficients: R2Tv = 0.910 for Trametes versicolor and R2Gt = 0.926 for Gloeophyllun trabeum. Small errors between the experimental and calculated values of two designed compounds indicated that these two QSAR models have strong predictability and stability.

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

    Science.gov (United States)

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

    2014-03-15

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

  15. Quantitative differences in think tank dissemination activities in Germany, Denmark and the UK

    DEFF Research Database (Denmark)

    Kelstrup, Jesper Dahl

    2017-01-01

    controlled for the number of full-time staff. The study indicates that factors beyond the policy process such as developments of funding and media environments should be analysed further as they are likely to be important for how and where think tank disseminate their policy advice....... research on think and the study of policy advice by arguing for a focus on the dissemination of policy advice by asking how the dissemination activities of think tanks vary across different policy advisory systems and what this implies for the study of policy advice. This question is explored...... in a quantitative design which compares publications, events and newspaper mentionings of samples of think tanks from a coordinated (Germany), liberal (UK) and mixed (Denmark) system in 2012. The analysis indicates that think tanks in the UK have the highest level of dissemination on all three activities when...

  16. Identifying hazard parameter to develop quantitative and dynamic hazard map of an active volcano in Indonesia

    Science.gov (United States)

    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.

  17. Bi-temporal 3D active appearance models with applications to unsupervised ejection fraction estimation

    DEFF Research Database (Denmark)

    Stegmann, Mikkel Bille; Pedersen, Dorthe

    2005-01-01

    Rapid and unsupervised quantitative analysis is of utmost importance to ensure clinical acceptance of many examinations using cardiac magnetic resonance imaging (MRI). We present a framework that aims at fulfilling these goals for the application of left ventricular ejection fraction estimation i...

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

    Science.gov (United States)

    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

  19. A new quantitative method to measure activity of ice structuring proteins using differential scanning calorimetry.

    Science.gov (United States)

    Hassa-Roudsari, Majid; Goff, H Douglas

    2012-01-01

    There are very few quantitative assays to measure the activity of antifreeze proteins (AFPs, or Ice Structuring Proteins, ISPs) and these can be prone to various inaccuracies and inconsistencies. Some methods rely only on unassisted visual assessment. When microscopy is used to measure ice crystal size, it is critical that standardized procedures be adopted, especially when image analysis software is used to quantify sizes. Differential Scanning Calorimetry (DSC) has been used to measure the thermal hysteresis activity (TH) of AFPs. In this study, DSC was used isothermally to measure enthalpic changes associated with structural rearrangements as a function of time. Differences in slopes of isothermal heat flow vs. time between winter wheat ISP or AFP type I containing samples, and those without ISP or AFP type I were demonstrated. ISP or AFP type I containing samples had significantly higher slopes compared to those without ISP or AFP type I. Samples with higher concentration of ISP or AFP type I showed higher slope values during the first hour and took up to 3 hr to attain equilibrium. Differences were attributed to activity of the proteins at the ice interface. Proteinaceous activity of ISPs or AFP type I was confirmed by loss of activity after treatment with protease.

  20. Quantitative structure-activity relationships of mutagenic activity from quantum topological descriptors: triazenes and halogenated hydroxyfuranones (mutagen-X) derivatives.

    Science.gov (United States)

    Popelier, P L A; Smith, P J; Chaudry, U A

    2004-11-01

    The mutagenic activity of 23 triazenes and, in a different set, of 24 halogenated hydroxyfuranones (MX derivatives) is quantitatively related to new features of contemporary molecular wave functions. Nowadays affordable computers are powerful enough to rapidly generate geometry-optimised ab initio wave functions at HF/3-21G*, HF/6-31G* and B3LYP/6-311 + G(2d,p) level for all molecules. The bonds of a common molecular skeleton are described by their ab initio bond lengths and local properties provided by the theory of quantum chemical topology (QCT). The chemometric analysis involves two types: one to generate a statistically validated quantitative model, and one to isolate the active center. In the former a genetic algorithm (GA) selects bond descriptors in order to optimise the cross-validation error, q2, followed by a full partial least squares (PLS) analysis, which also yields randomisation statistics. In the latter type principal components (PCs) are constructed from the original bond descriptors and their variables important to the projection (VIPs) are plotted in a histogram. This analysis suggests a preferred mechanistic pathway for the initial hydroxylation of the triazenes, an issue that has remained ambiguous so far. In the case of the hydroxyfuranones the proposed method aids the elucidation of a mechanistic ambivalence.

  1. The Estimation of Cortical Activity for Brain-Computer Interface: Applications in a Domotic Context

    OpenAIRE

    Babiloni, F.; Cincotti, F; M. Marciani; Salinari, S.; Astolfi, L.; A. Tocci; Aloise, F.; De Mattia, D.; De Vico Fallani, F.; Bufalari, S.

    2007-01-01

    In order to analyze whether the use of the cortical activity, estimated from noninvasive EEG recordings, could be useful to detect mental states related to the imagination of limb movements, we estimate cortical activity from high-resolution EEG recordings in a group of healthy subjects by using realistic head models. Such cortical activity was estimated in region of interest associated with the subject's Brodmann areas by using a depth-weighted minimum norm...

  2. Effects of calibration methods on quantitative material decomposition in photon-counting spectral computed tomography using a maximum a posteriori estimator.

    Science.gov (United States)

    Curtis, Tyler E; Roeder, Ryan K

    2017-07-06

    Advances in photon-counting detectors have enabled quantitative material decomposition using multi-energy or spectral computed tomography (CT). Supervised methods for material decomposition utilize an estimated attenuation for each material of interest at each photon energy level, which must be calibrated based upon calculated or measured values for known compositions. Measurements using a calibration phantom can advantageously account for system-specific noise, but the effect of calibration methods on the material basis matrix and subsequent quantitative material decomposition has not been experimentally investigated. Therefore, the objective of this study was to investigate the influence of the range and number of contrast agent concentrations within a modular calibration phantom on the accuracy of quantitative material decomposition in the image domain. Gadolinium was chosen as a model contrast agent in imaging phantoms, which also contained bone tissue and water as negative controls. The maximum gadolinium concentration (30, 60, and 90 mM) and total number of concentrations (2, 4, and 7) were independently varied to systematically investigate effects of the material basis matrix and scaling factor calibration on the quantitative (root mean squared error, RMSE) and spatial (sensitivity and specificity) accuracy of material decomposition. Images of calibration and sample phantoms were acquired using a commercially available photon-counting spectral micro-CT system with five energy bins selected to normalize photon counts and leverage the contrast agent k-edge. Material decomposition of gadolinium, calcium, and water was performed for each calibration method using a maximum a posteriori estimator. Both the quantitative and spatial accuracy of material decomposition were most improved by using an increased maximum gadolinium concentration (range) in the basis matrix calibration; the effects of using a greater number of concentrations were relatively small in

  3. A quantitative structure-activity relationship study of anti-HIV activity of substituted HEPT using nonlinear models.

    Science.gov (United States)

    Noorizadeh, Hadi; Sajjadifar, Sami; Farmany, Abbas

    2013-01-01

    We performed studies on extended series of 79 HEPT ligands (1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine), inhibitors of HIV reverse-transcriptase with anti-HIV biological activity, using quantitative structure-activity relationship (QSAR) methods that imply analysis of correlations and representation of models. A suitable set of molecular descriptors was calculated, and the genetic algorithm was employed to select those descriptors which resulted in the best-fit models. The kernel partial least square and Levenberg-Marquardt artificial neural network were utilized to construct the nonlinear QSAR models. The proposed methods will be of great significance in this research, and would be expected to apply to other similar research fields.

  4. Voltage Estimation in Active Distribution Grids Using Neural Networks

    DEFF Research Database (Denmark)

    Pertl, Michael; Heussen, Kai; Gehrke, Oliver

    2016-01-01

    the observability of distribution systems has to be improved. To increase the situational awareness of the power system operator data driven methods can be employed. These methods benefit from newly available data sources such as smart meters. This paper presents a voltage estimation method based on neural networks...

  5. Health game interventions to enhance physical activity self-efficacy of children: a quantitative systematic review.

    Science.gov (United States)

    Pakarinen, Anni; Parisod, Heidi; Smed, Jouni; Salanterä, Sanna

    2017-04-01

    To describe and explore health game interventions that enhance the physical activity self-efficacy of children and to evaluate the effectiveness of these interventions. Physical inactivity among children has increased globally. Self-efficacy is one of the key determinants of physical activity engagement in children. There is a need to explore new and innovative interventions to enhance physical activity self-efficacy that are also acceptable for today's children. Quantitative systematic review. MEDLINE (Ovid), CINAHL, PsychInfo, EMBASE and the Cochrane Library between 1996-2016. A review was conducted in accordance with the Cochrane Collaboration guidelines. A systematic search was done in June 2016 by two independent reviewers according to the eligibility criteria as follows: controlled trial, comparison of digital game intervention with no game intervention control condition, participants younger than 18 years of age and reported statistical analyses of a physical activity self-efficacy outcome measure. Altogether, five studies met the eligibility criteria. Four game interventions, employing three active games and one educational game, had positive effects on children's physical activity self-efficacy. An intervention, employing a game-themed mobile application, showed no intervention effects. The variation between intervention characteristics was significant and the quality of the studies was found to be at a medium level. Although health game interventions seemingly enhance the physical activity self-efficacy of children and have potential as a means of increasing physical activity, more rigorous research is needed to clarify how effective such interventions are in the longer run to contribute to the development of game-based interventions. © 2016 John Wiley & Sons Ltd.

  6. Quantitative coronary angiography in the estimation of the functional significance of coronary stenosis: correlations with dobutamine-atropine stress test

    NARCIS (Netherlands)

    J.M.P. Baptista da Silva (José); M. Arnese (Mariarosaria); J.R.T.C. Roelandt (Jos); P.M. Fioretti (Paolo); D.T.J. Keane (David); J. Escaned (Javier); C. di Mario (Carlo); P.W.J.C. Serruys (Patrick); H. Boersma (Eric)

    1994-01-01

    textabstractOBJECTIVES. The purpose of this study was to determine the predictive value of quantitative coronary angiography in the assessment of the functional significance of coronary stenosis as judged from the development of left ventricular wall motion abnormalities during dobutamine-atropine

  7. Quantitative estimation of the influence of external vibrations on the measurement error of a coriolis mass-flow meter

    NARCIS (Netherlands)

    Ridder, van de L.; Hakvoort, W.B.J.; Dijk, van J.; Lötters, J.C.; Boer, de A.; Dimitrovova, Z.; Almeida, de J.R.

    2013-01-01

    In this paper the quantitative influence of external vibrations on the measurement value of a Coriolis Mass-Flow Meter for low flows is investigated, with the eventual goal to reduce the influence of vibrations. Model results are compared with experimental results to improve the knowledge on how ext

  8. Quantitative approaches for health risk assessment of environmental pollutants : estimation of differences in sensitivity, relative potencies, and margins of exposure

    OpenAIRE

    Kalantari, Fereshteh

    2012-01-01

    Historically, quantitative health risk assessment of chemical substances is based on deterministic approaches. For a more realistic and informative health risk assessment, however, the variability and uncertainty inherent in measurements should be taken into consideration. The variability and uncertainty may be assessed by applying probabilistic methods when performing dose-response assessment, exposure assessment and risk characterization. The benchmark dose (BMD) method has b...

  9. Quantitative coronary angiography in the estimation of the functional significance of coronary stenosis: correlations with dobutamine-atropine stress test

    NARCIS (Netherlands)

    J.M.P. Baptista da Silva (José); M. Arnese (Mariarosaria); J.R.T.C. Roelandt (Jos); P.M. Fioretti (Paolo); D.T.J. Keane (David); J. Escaned (Javier); C. di Mario (Carlo); P.W.J.C. Serruys (Patrick); H. Boersma (Eric)

    1994-01-01

    textabstractOBJECTIVES. The purpose of this study was to determine the predictive value of quantitative coronary angiography in the assessment of the functional significance of coronary stenosis as judged from the development of left ventricular wall motion abnormalities during dobutamine-atropine s

  10. Visualization of plant viral suppressor silencing activity in intact leaf lamina by quantitative fluorescent imaging

    Directory of Open Access Journals (Sweden)

    Francis Kevin P

    2011-08-01

    Full Text Available Abstract Background Transient expression of proteins in plants has become a favoured method over the production of stably transformed plants because, in addition to enabling high protein yields, it is both fast and easy to apply. An enhancement of transient protein expression can be achieved by plant virus-encoded RNA silencing suppressor proteins. Since viral suppressor proteins differ in their efficiency to enhance transient protein expression in plants, we developed a whole-leaf green fluorescent protein (GFP-based imaging assay to quantitatively assess suppressor protein activity. Results In a transient GFP-expression assay using wild-type and GFP-transgenic N. benthamiana, addition of the plant viral suppressors Beet mild yellowing virus (BMYV-IPP P0 or Plum pox virus (PPV HC-Pro was shown to increase fluorescent protein expression 3-4-fold, 7 days post inoculation (dpi when compared to control plants. In contrast, in agroinfiltrated patches without suppressor activity, near complete silencing of the GFP transgene was observed in the transgenic N. benthamiana at 21 dpi. Both co-infiltrated suppressors significantly enhanced GFP expression over time, with HC-Pro co-infiltrations leading to higher short term GFP fluorescence (at 7 dpi and P0 giving higher long term GFP fluorescence (at 21 dpi. Additionally, in contrast to HC-Pro co-infiltrations, an area of complete GFP silencing was observed at the edge of P0 co-infiltrated areas. Conclusions Fluorescence imaging of whole intact leaves proved to be an easy and effective method for spatially and quantitatively observing viral suppressor efficiency in plants. This suppressor assay demonstrates that plant viral suppressors greatly enhanced transient GFP expression, with P0 showing a more prolonged suppressor activity over time than HC-Pro. Both suppressors could prove to be ideal candidates for enhancing target protein expression in plants.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  12. Technology Efficacy in Active Prosthetic Knees for Transfemoral Amputees: A Quantitative Evaluation

    Directory of Open Access Journals (Sweden)

    Amr M. El-Sayed

    2014-01-01

    Full Text Available 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.

  13. Estimating the economic impact of seismic activity in Kyrgyzstan

    Science.gov (United States)

    Pittore, Massimiliano; Sousa, Luis; Grant, Damian; Fleming, Kevin; Parolai, Stefano; Free, Matthew; Moldobekov, Bolot; Takeuchi, Ko

    2017-04-01

    Estimating the short and long-term economical impact of large-scale damaging events such as earthquakes, tsunamis or tropical storms is an important component of risk assessment, whose outcomes are routinely used to improve risk awareness, optimize investments in prevention and mitigation actions, as well as to customize insurance and reinsurance rates to specific geographical regions or single countries. Such estimations can be carried out by modeling the whole causal process, from hazard assessment to the estimation of loss for specific categories of assets. This approach allows a precise description of the various physical mechanisms contributing to direct seismic losses. However, it should reflect the underlying epistemic and random uncertainties in all involved components in a meaningful way. Within a project sponsored by the World Bank, a seismic risk study for the Kyrgyz Republic has been conducted, focusing on the assessment of social and economical impacts assessed in terms of direct losses of the residential and public building stocks. Probabilistic estimates based on stochastic event catalogs have been computed and integrated with the simulation of specific earthquake scenarios. Although very few relevant data are available in the region on the economic consequences of past damaging events, the proposed approach sets a benchmark for decision makers and policy holders to better understand the short and long term consequences of earthquakes in the region. The presented results confirm the high level of seismic risk of the Kyrgyz Republic territory, outlining the most affected regions; thus advocating for significant Disaster Risk Reduction (DRR) measures to be implemented by local decision- and policy-makers.

  14. The MSFC Solar Activity Future Estimation (MSAFE) Model

    Science.gov (United States)

    Suggs, Ron

    2017-01-01

    The Natural Environments Branch of the Engineering Directorate at Marshall Space Flight Center (MSFC) provides solar cycle forecasts for NASA space flight programs and the aerospace community. These forecasts provide future statistical estimates of sunspot number, solar radio 10.7 cm flux (F10.7), and the geomagnetic planetary index, Ap, for input to various space environment models. For example, many thermosphere density computer models used in spacecraft operations, orbital lifetime analysis, and the planning of future spacecraft missions require as inputs the F10.7 and Ap. The solar forecast is updated each month by executing MSAFE using historical and the latest month's observed solar indices to provide estimates for the balance of the current solar cycle. The forecasted solar indices represent the 13-month smoothed values consisting of a best estimate value stated as a 50 percentile value along with approximate +/- 2 sigma values stated as 95 and 5 percentile statistical values. This presentation will give an overview of the MSAFE model and the forecast for the current solar cycle.

  15. Quantitative estimation of bioclimatic parameters from presence/absence vegetation data in North America by the modern analog technique

    Science.gov (United States)

    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.

  16. A quantitative magnetic resonance histology atlas of postnatal rat brain development with regional estimates of growth and variability.

    Science.gov (United States)

    Calabrese, Evan; Badea, Alexandra; Watson, Charles; Johnson, G Allan

    2013-05-01

    There has been growing interest in the role of postnatal brain development in the etiology of several neurologic diseases. The rat has long been recognized as a powerful model system for studying neuropathology and the safety of pharmacologic treatments. However, the complex spatiotemporal changes that occur during rat neurodevelopment remain to be elucidated. This work establishes the first magnetic resonance histology (MRH) atlas of the developing rat brain, with an emphasis on quantitation. The atlas comprises five specimens at each of nine time points, imaged with eight distinct MR contrasts and segmented into 26 developmentally defined brain regions. The atlas was used to establish a timeline of morphometric changes and variability throughout neurodevelopment and represents a quantitative database of rat neurodevelopment for characterizing rat models of human neurologic disease. Published by Elsevier Inc.

  17. Quantitative structure-activity relationship study on the biodegradation of acid dyestuffs

    Institute of Scientific and Technical Information of China (English)

    LI Yin; XI Dan-li

    2007-01-01

    Quantitative structure-biodegradability relationships (QSBRs) were established to develop predictive models and mechanistic explanations for acid dyestuffs as well as biological activities. With a total of four descriptors, molecular weight (MW), energies of the highest occupied molecular orbital (EHOMO), the lowest unoccupied molecular orbital (ELUMO), and the excited state (EES), calculated using quantum chemical semi-empirical methodology, a series of models were analyzed between the dye biodegradability and each descriptor. Results showed that EHOMO and MW were the dominant parameters controlling the biodegradability of acid dyes. A statistically robust QSBR model was developed for all studied dyes, with the combined application of EHOMO and MW. The calculated biodegradations fitted well with the experimental data monitored in a facultative-aerobic process, indicative of the reliable prediction and mechanistic character of the developed model.

  18. New Quantitative Structure-Activity Relationship Models Improve Predictability of Ames Mutagenicity for Aromatic Azo Compounds.

    Science.gov (United States)

    Manganelli, Serena; Benfenati, Emilio; Manganaro, Alberto; Kulkarni, Sunil; Barton-Maclaren, Tara S; Honma, Masamitsu

    2016-10-01

    Existing Quantitative Structure-Activity Relationship (QSAR) models have limited predictive capabilities for aromatic azo compounds. In this study, 2 new models were built to predict Ames mutagenicity of this class of compounds. The first one made use of descriptors based on simplified molecular input-line entry system (SMILES), calculated with the CORAL software. The second model was based on the k-nearest neighbors algorithm. The statistical quality of the predictions from single models was satisfactory. The performance further improved when the predictions from these models were combined. The prediction results from other QSAR models for mutagenicity were also evaluated. Most of the existing models were found to be good at finding toxic compounds but resulted in many false positive predictions. The 2 new models specific for this class of compounds avoid this problem thanks to a larger set of related compounds as training set and improved algorithms.

  19. Quantitation of the receptor for urokinase plasminogen activator by enzyme-linked immunosorbent assay

    DEFF Research Database (Denmark)

    Rønne, E; Behrendt, N; Ploug, M;

    1994-01-01

    variant of uPAR, suPAR, has been constructed by recombinant technique and the protein content of a purified suPAR standard preparation was determined by amino acid composition analysis. The sensitivity of the assay (0.6 ng uPAR/ml) is strong enough to measure uPAR in extracts of cultured cells and cancer......Binding of the urokinase plasminogen activator (uPA) to a specific cell surface receptor (uPAR) plays a crucial role in proteolysis during tissue remodelling and cancer invasion. An immunosorbent assay for the quantitation of uPAR has now been developed. This assay is based on two monoclonal...... tissue. Recent studies have shown that a high uPA level in tumor extracts is in some cancers associated with poor prognosis. The present assay will now allow similar prognostic studies of uPAR levels....

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

    CERN Document Server

    Shin, Seungwoo; Yoon, Jonghee; Park, YongKeun

    2015-01-01

    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 two-dimensional synthetic aperture phase image and a three-dimensional 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, including a human red blood cell and a HeLa cell.

  1. Quantitative super-resolution imaging of Bruchpilot distinguishes active zone states.

    Science.gov (United States)

    Ehmann, Nadine; van de Linde, Sebastian; Alon, Amit; Ljaschenko, Dmitrij; Keung, Xi Zhen; Holm, Thorge; Rings, Annika; DiAntonio, Aaron; Hallermann, Stefan; Ashery, Uri; Heckmann, Manfred; Sauer, Markus; Kittel, Robert J

    2014-08-18

    The precise molecular architecture of synaptic active zones (AZs) gives rise to different structural and functional AZ states that fundamentally shape chemical neurotransmission. However, elucidating the nanoscopic protein arrangement at AZs is impeded by the diffraction-limited resolution of conventional light microscopy. Here we introduce new approaches to quantify endogenous protein organization at single-molecule resolution in situ with super-resolution imaging by direct stochastic optical reconstruction microscopy (dSTORM). Focusing on the Drosophila neuromuscular junction (NMJ), we find that the AZ cytomatrix (CAZ) is composed of units containing ~137 Bruchpilot (Brp) proteins, three quarters of which are organized into about 15 heptameric clusters. We test for a quantitative relationship between CAZ ultrastructure and neurotransmitter release properties by engaging Drosophila mutants and electrophysiology. Our results indicate that the precise nanoscopic organization of Brp distinguishes different physiological AZ states and link functional diversification to a heretofore unrecognized neuronal gradient of the CAZ ultrastructure.

  2. Investigations on abundance and activity of microbial sponge symbionts using quantitative real - time PCR

    DEFF Research Database (Denmark)

    Kumala, Lars; Hentschel, Ute; Bayer, Kristina

    Marine sponges are hosts to dense and diverse microbial consortia that are likely to play a key role in the metabolic processes of the host sponge due to their enormous abundance. Common symbioses between nitrogen transforming microorganisms and sponges indicate complex nitrogen cycling within...... the host. Of particular interest is determining the community structure and function of microbial symbionts in order to gain deeper insight into host-symbiont interactions. We investigated the abundance and activity of microbial symbionts in two Mediterranean sponge species using quantitative real-time PCR....... An absolute quantification of functional genes and transcripts in archaeal and bacterial symbionts was conducted to determine their involvement in nitrification and denitrification, comparing the low microbial abundance (LMA) sponge Dysidea avara with the high microbial abundance (HMA) representative Aplysina...

  3. A descriptor of amino acids: SVRG and its application to peptide quantitative structure-activity relationship.

    Science.gov (United States)

    Tong, J; Che, T; Li, Y; Wang, P; Xu, X; Chen, Y

    2011-01-01

    In this work, a descriptor, SVRG (principal component scores vector of radial distribution function descriptors and geometrical descriptors), was derived from principal component analysis (PCA) of a matrix of two structural variables of coded amino acids, including radial distribution function index (RDF) and geometrical index. SVRG scales were then applied in three panels of peptide quantitative structure-activity relationships (QSARs) which were modelled by partial least squares regression (PLS). The obtained models with the correlation coefficient (R²(cum)), cross-validation correlation coefficient (Q²(LOO)) were 0.910 and 0.863 for 48 bitter-tasting dipeptides; 0.968 and 0.931 for 21 oxytocin analogues; and 0.992 and 0.954 for 20 thromboplastin inhibitors. Satisfactory results showed that SVRG contained much chemical information relating to bioactivities. The approach may be a useful structural expression methodology for studies on peptide QSAR.

  4. Partial least squares modeling and genetic algorithm optimization in quantitative structure-activity relationships.

    Science.gov (United States)

    Hasegawa, K; Funatsu, K

    2000-01-01

    Quantitative structure-activity relationship (QSAR) studies based on chemometric techniques are reviewed. Partial least squares (PLS) is introduced as a novel robust method to replace classical methods such as multiple linear regression (MLR). Advantages of PLS compared to MLR are illustrated with typical applications. Genetic algorithm (GA) is a novel optimization technique which can be used as a search engine in variable selection. A novel hybrid approach comprising GA and PLS for variable selection developed in our group (GAPLS) is described. The more advanced method for comparative molecular field analysis (CoMFA) modeling called GA-based region selection (GARGS) is described as well. Applications of GAPLS and GARGS to QSAR and 3D-QSAR problems are shown with some representative examples. GA can be hybridized with nonlinear modeling methods such as artificial neural networks (ANN) for providing useful tools in chemometric and QSAR.

  5. In vivo toxicity of nitroaromatics: A comprehensive quantitative structure-activity relationship study.

    Science.gov (United States)

    Gooch, Aminah; Sizochenko, Natalia; Rasulev, Bakhtiyor; Gorb, Leonid; Leszczynski, Jerzy

    2017-02-07

    The toxicity data of 90 nitroaromatic compounds related to their 50% lethal dose concentration for rats (LD50) were analyzed to develop quantitative structure-activity relationship (QSAR) models. Quantum-chemically calculated descriptors together with molecular descriptors generated by DRAGON, PaDEL, and HiT-QSAR software were utilized to build QSAR models. Quality and validity of the models were determined by internal and external validation techniques. The results show that the toxicity of nitroaromatic compounds depends on various factors, such as the number of nitro-groups, the topological state, and the presence of certain structural fragments. The developed models based on the largest (to date) dataset of nitroaromatics in vivo toxicity showed a good predictive ability. The results provide important input that could be applied in a preliminary assessment of nitroaromatic compounds' toxicity to mammals. Environ Toxicol Chem 2017;9999:1-7. © 2017 SETAC.

  6. Quantitative structure property relationships for the adsorption of pharmaceuticals onto activated carbon.

    Science.gov (United States)

    Dickenson, E R V; Drewes, J E

    2010-01-01

    Isotherms were determined for the adsorption of five pharmaceutical residues, primidone, carbamazepine, ibuprofen, naproxen and diclofenac, to Calgon Filtrasorb 300 powdered activated carbon (PAC). The sorption behavior was examined in ultra-pure and wastewater effluent organic matter (EfOM) matrices, where more sorption was observed in the ultra-pure water for PAC doses greater than 10 mg/L suggesting the presence of EfOM hinders the sorption of the pharmaceuticals to the PAC. Adsorption behaviors were described by the Freundlich isotherm model. Quantitative structure property relationships (QSPRs) in the form of polyparameter linear solvation energy relationships were developed for simulating the Freundlich adsorption capacity in both ultra-pure and EfOM matrices. The significant 3D-based descriptors for the QSPRs were the molar volume, polarizability and hydrogen-bond donor parameters.

  7. Quantitative impedimetric NPY-receptor activation monitoring and signal pathway profiling in living cells.

    Science.gov (United States)

    te Kamp, Verena; Lindner, Ricco; Jahnke, Heinz-Georg; Krinke, Dana; Kostelnik, Katja B; Beck-Sickinger, Annette G; Robitzki, Andrea A

    2015-05-15

    Label-free and non-invasive monitoring of receptor activation and identification of the involved signal pathways in living cells is an ongoing analytic challenge and a great opportunity for biosensoric systems. In this context, we developed an impedance spectroscopy-based system for the activation monitoring of NPY-receptors in living cells. Using an optimized interdigital electrode array for sensitive detection of cellular alterations, we were able for the first time to quantitatively detect the NPY-receptor activation directly without a secondary or enhancer reaction like cAMP-stimulation by forskolin. More strikingly, we could show that the impedimetric based NPY-receptor activation monitoring is not restricted to the Y1-receptor but also possible for the Y2- and Y5-receptor. Furthermore, we could monitor the NPY-receptor activation in different cell lines that natively express NPY-receptors and proof the specificity of the observed impedimetric effect by agonist/antagonist studies in recombinant NPY-receptor expressing cell lines. To clarify the nature of the observed impedimetric effect we performed an equivalent circuit analysis as well as analyzed the role of cell morphology and receptor internalization. Finally, an antagonist based extensive molecular signal pathway analysis revealed small alterations of the actin cytoskeleton as well as the inhibition of at least L-type calcium channels as major reasons for the observed NPY-induced impedance increase. Taken together, our novel impedance spectroscopy based NPY-receptor activation monitoring system offers the opportunity to identify signal pathways as well as for novel versatile agonist/antagonist screening systems for identification of novel therapeutics in the field of obesity and cancer.

  8. Quantitative analysis of catechins in Saraca asoca and correlation with antimicrobial activity

    Institute of Scientific and Technical Information of China (English)

    Amey Shirolkar; Anjum Gahlaut; Anil K. Chhillar; Rajesh Dabur

    2013-01-01

    Herbal medicines are highly complex and have unknown mechanisms in diseases treatment. Saraca asoca (Roxb.), De. Wild has been recommended to treat gynecological disorders and used in several commercial polyherbal formulations. In present study, efforts have been made to explore antimicrobial activity and its co-relation with the distributions of catechins in the organs of S. asoca using targeted MS/MS. Eight extracts (cold and hot water) from four different organs of S. asoca and two drugs were prepared and antimicrobial activity was assessed by microbroth dilution assay. Quantitative and qualitative analysis of catechins in crude extracts was done by using targeted and auto-MS/MS and correlated with antimicrobial activity. (þ)-Catechin and (þ)-epicatechin and their biosynthesis related compound were found to be up-regulated in regenerated bark and leaves extracts. (?)-Epigallocatechin was found to be significantly higher in bark water extract as compared to others but showed low antimicrobial activity. Result showed down-regulation of (?)-epigallocatechin and up-regulation of (þ)-catechin and (þ)-epicatechin in the regenerated bark and leaves of S. asoca. It might be the contributing factor in the antimicrobial activity of regenerated bark and leaves of the plant. The concentration of (þ)-epicatechin in processed drugs (Ashokarishta) from Baidyanath was found to be seven times higher than that of Dabur Pvt. Ltd., but no antimicrobial activity was observed, indicating the variations among the plant based drugs. This will be helpful in rational use of S. asoca parts. Furthermore, the analytical method developed is sensitive, repeatable and reliable; therefore, it is suitable for quality control of herbal drugs.

  9. Variant for estimating the activity of tropical cyclone groups in the world ocean

    Science.gov (United States)

    Yaroshevich, M. I.

    2016-12-01

    It is especially important to know the character and the intensity level of tropical cyclone (TC) activity when the system for estimating the cyclonic danger and risk is formed. During seasons of increased cyclonic activity, when several TCs are simultaneously active, the total energy effect of the cyclone group joint action is not estimated numerically. Cyclonic activity is as a rule characterized by the number of TCs that occur in the considered zone. A variant of the criterion, according to which relative cyclonic activity is estimated, is presented.

  10. 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.

    Science.gov (United States)

    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

  11. Quantitative detection of powdered activated carbon in wastewater treatment plant effluent by thermogravimetric analysis (TGA).

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  13. A comparison of energy expenditure estimation of several physical activity monitors.

    Science.gov (United States)

    Dannecker, Kathryn L; Sazonova, Nadezhda A; Melanson, Edward L; Sazonov, Edward S; Browning, Raymond C

    2013-11-01

    Accurately and precisely estimating free-living energy expenditure (EE) is important for monitoring energy balance and quantifying physical activity. Recently, single and multisensor devices have been developed that can classify physical activities, potentially resulting in improved estimates of EE. This study aimed to determine the validity of EE estimation of a footwear-based physical activity monitor and to compare this validity against a variety of research and consumer physical activity monitors. Nineteen healthy young adults (10 men, 9 women) completed a 4-h stay in a room calorimeter. Participants wore a footwear-based physical activity monitor as well as Actical, ActiGraph, IDEEA, DirectLife, and Fitbit devices. Each individual performed a series of postures/activities. We developed models to estimate EE from the footwear-based device, and we used the manufacturer's software to estimate EE for all other devices. Estimated EE using the shoe-based device was not significantly different than measured EE (mean ± SE; 476 ± 20 vs 478 ± 18 kcal, respectively) and had a root-mean-square error of 29.6 kcal (6.2%). The IDEEA and the DirectLlife estimates of EE were not significantly different than the measured EE, but the ActiGraph and the Fitbit devices significantly underestimated EE. Root-mean-square errors were 93.5 (19%), 62.1 kcal (14%), 88.2 kcal (18%), 136.6 kcal (27%), 130.1 kcal (26%), and 143.2 kcal (28%) for Actical, DirectLife, IDEEA, ActiGraph, and Fitbit, respectively. The shoe-based physical activity monitor provides a valid estimate of EE, whereas the other physical activity monitors tested have a wide range of validity when estimating EE. Our results also demonstrate that estimating EE based on classification of physical activities can be more accurate and precise than estimating EE based on total physical activity.

  14. Quantitative structure-activity relationships of selected phenols with non-monotonic dose-response curves

    Institute of Scientific and Technical Information of China (English)

    GAO ChangAn; ZHANG AiQian; LIN Yuan; YIN DaQiang; WANG LianSheng

    2009-01-01

    Particular non-monotonic dose-response curves of many endocrine disrupting chemicals (EDCs) suggest the existence of diverse toxicity mechanisms at different dose levels. As a result, the biologi-cal activities of EDCs cannot be simply exhibited by unique EC/LD<,50. values, and the quantitative structure-activity relationship (QSAR) analysis for non-monotonic dose-response relationship be-comes an unknown field in the environmental science. In this paper, nine phenols with inverted U-shaped dose-response curves in lymphocyte proliferation test of Carassius auratus were selected. The binding interactions between the phenols and several typical EDCs-related receptors were then explored in a molecular simulation study. The estrogen receptor (ER), androgen receptor (AR), thyroid hormone receptor (TR), bacterial O2 sensing FixL protein (FixL), aryl hydrocarbon receptor (AhR), and the peroxisome proliferator-activated receptor (PPAR) were the target receptors in the study. Linear regression QSAR models for the low and high exposure levels of the compounds were developed separately. The results indicated that the lymphocyte proliferation in the low-dose range might involve ER-mediated process, while the proliferation inhibition in the high dose range was dominated by the acute toxicity of phenols due to receptor occupancy and cell damage.

  15. A quantitative infection assay for human type I, II, and III interferon antiviral activities

    Science.gov (United States)

    2013-01-01

    Background Upon virus infection, cells secrete a diverse group of antiviral molecules that signal proximal cells to enter into an antiviral state, slowing or preventing viral spread. These paracrine signaling molecules can work synergistically, so measurement of any one antiviral molecule does not reflect the total antiviral activity of the system. Results We have developed an antiviral assay based on replication inhibition of an engineered fluorescent vesicular stomatitis virus reporter strain on A549 human lung epithelial cells. Our assay provides a quantitative functional readout of human type I, II, and III interferon activities, and it provides better sensitivity, intra-, and inter-assay reproducibility than the traditional crystal violet based assay. Further, it eliminates cell fixation, rinsing, and staining steps, and is inexpensive to implement. Conclusions A dsRed2-strain of vesicular stomatitis virus that is sensitive to type I, II, and III interferons was used to develop a convenient and sensitive assay for interferon antiviral activity. We demonstrate use of the assay to quantify the kinetics of paracrine antiviral signaling from human prostate cancer (PC3) cells in response to viral infection. The assay is applicable to high-throughput screening for anti-viral compounds as well as basic studies of cellular antiviral signaling. PMID:23829314

  16. Structural parameterization and functional prediction of antigenic polypeptome sequences with biological activity through quantitative sequence-activity models (QSAM) by molecular electronegativity edge-distance vector (VMED)

    Institute of Scientific and Technical Information of China (English)

    LI; ZhiLiang; WU; ShiRong; CHEN; ZeCong; YE; Nancy; YANG; ShengXi; LIAO; ChunYang; ZHANG; MengJun; YANG; Li; MEI; Hu; YANG; Yan; ZHAO; Na; ZHOU; Yuan; ZHOU; Ping; XIONG; Qing; XU; Hong; LIU; ShuShen; LING; ZiHua; CHEN; Gang; LI; GenRong

    2007-01-01

    Only from the primary structures of peptides, a new set of descriptors called the molecular electronegativity edge-distance vector (VMED) was proposed and applied to describing and characterizing the molecular structures of oligopeptides and polypeptides, based on the electronegativity of each atom or electronic charge index (ECI) of atomic clusters and the bonding distance between atom-pairs. Here, the molecular structures of antigenic polypeptides were well expressed in order to propose the automated technique for the computerized identification of helper T lymphocyte (Th) epitopes. Furthermore, a modified MED vector was proposed from the primary structures of polypeptides, based on the ECI and the relative bonding distance of the fundamental skeleton groups. The side-chains of each amino acid were here treated as a pseudo-atom. The developed VMED was easy to calculate and able to work. Some quantitative model was established for 28 immunogenic or antigenic polypeptides (AGPP) with 14 (1―14) Ad and 14 other restricted activities assigned as "1"(+) and "0"(-), respectively. The latter comprised 6 Ab(15-20), 3 Ak(21-23), 2 Ek(24-26), 2 H-2k(27 and 28) restricted sequences. Good results were obtained with 90% correct classification (only 2 wrong ones for 20 training samples) and 100% correct prediction (none wrong for 8 testing samples); while contrastively 100% correct classification (none wrong for 20 training samples) and 88% correct classification (1 wrong for 8 testing samples). Both stochastic samplings and cross validations were performed to demonstrate good performance. The described method may also be suitable for estimation and prediction of classes I and II for major histocompatibility antigen (MHC) epitope of human. It will be useful in immune identification and recognition of proteins and genes and in the design and development of subunit vaccines. Several quantitative structure activity relationship (QSAR) models were developed for various

  17. Quantitatively accurate activity measurements with a dedicated cardiac SPECT camera: Physical phantom experiments

    Energy Technology Data Exchange (ETDEWEB)

    Pourmoghaddas, Amir, E-mail: apour@ottawaheart.ca; Wells, R. Glenn [Physics Department, Carleton University, Ottawa, Ontario K1S 5B6, Canada and Cardiology, The University of Ottawa Heart Institute, Ottawa, Ontario K1Y4W7 (Canada)

    2016-01-15

    Purpose: Recently, there has been increased interest in dedicated cardiac single photon emission computed tomography (SPECT) scanners with pinhole collimation and improved detector technology due to their improved count sensitivity and resolution over traditional parallel-hole cameras. With traditional cameras, energy-based approaches are often used in the clinic for scatter compensation because they are fast and easily implemented. Some of the cardiac cameras use cadmium-zinc-telluride (CZT) detectors which can complicate the use of energy-based scatter correction (SC) due to the low-energy tail—an increased number of unscattered photons detected with reduced energy. Modified energy-based scatter correction methods can be implemented, but their level of accuracy is unclear. In this study, the authors validated by physical phantom experiments the quantitative accuracy and reproducibility of easily implemented correction techniques applied to {sup 99m}Tc myocardial imaging with a CZT-detector-based gamma camera with multiple heads, each with a single-pinhole collimator. Methods: Activity in the cardiac compartment of an Anthropomorphic Torso phantom (Data Spectrum Corporation) was measured through 15 {sup 99m}Tc-SPECT acquisitions. The ratio of activity concentrations in organ compartments resembled a clinical {sup 99m}Tc-sestamibi scan and was kept consistent across all experiments (1.2:1 heart to liver and 1.5:1 heart to lung). Two background activity levels were considered: no activity (cold) and an activity concentration 1/10th of the heart (hot). A plastic “lesion” was placed inside of the septal wall of the myocardial insert to simulate the presence of a region without tracer uptake and contrast in this lesion was calculated for all images. The true net activity in each compartment was measured with a dose calibrator (CRC-25R, Capintec, Inc.). A 10 min SPECT image was acquired using a dedicated cardiac camera with CZT detectors (Discovery NM530c, GE

  18. Probabilistic quantitative microbial risk assessment model of norovirus from wastewater irrigated vegetables in Ghana using genome copies and fecal indicator ratio conversion for estimating exposure dose

    DEFF Research Database (Denmark)

    Owusu-Ansah, Emmanuel de-Graft Johnson; Sampson, Angelina; Amponsah, Samuel K.

    2017-01-01

    The need to replace the commonly applied fecal indicator conversions ratio (an assumption of 1:10− 5 virus to fecal indicator organism) in Quantitative Microbial Risk Assessment (QMRA) with models based on quantitative data on the virus of interest has gained prominence due to the different...... physical and environmental factors that might influence the reliability of using indicator organisms in microbial risk assessment. The challenges facing analytical studies on virus enumeration (genome copies or particles) have contributed to the already existing lack of data in QMRA modelling. This study...... to estimate the norovirus count. In all scenarios of using different water sources, the application of the fecal indicator conversion ratio underestimated the norovirus disease burden, measured by the Disability Adjusted Life Years (DALYs), when compared to results using the genome copies norovirus data...

  19. The influence of the design matrix on treatment effect estimates in the quantitative analyses of single-subject experimental design research.

    Science.gov (United States)

    Moeyaert, Mariola; Ugille, Maaike; Ferron, John M; Beretvas, S Natasha; Van den Noortgate, Wim

    2014-09-01

    The quantitative methods for analyzing single-subject experimental data have expanded during the last decade, including the use of regression models to statistically analyze the data, but still a lot of questions remain. One question is how to specify predictors in a regression model to account for the specifics of the design and estimate the effect size of interest. These quantitative effect sizes are used in retrospective analyses and allow synthesis of single-subject experimental study results which is informative for evidence-based decision making, research and theory building, and policy discussions. We discuss different design matrices that can be used for the most common single-subject experimental designs (SSEDs), namely, the multiple-baseline designs, reversal designs, and alternating treatment designs, and provide empirical illustrations. The purpose of this article is to guide single-subject experimental data analysts interested in analyzing and meta-analyzing SSED data. © The Author(s) 2014.

  20. A Quantitative Structure Activity Relationship for acute oral toxicity of pesticides on rats: Validation, domain of application and prediction.

    Science.gov (United States)

    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.

  1. Predicting quantitative structure-activity relationship of substituted 17α-acetoxyprogesterones by molecular hybridization electronegativity-distance vector

    Institute of Scientific and Technical Information of China (English)

    SUN Li-li; LAN Yu-kun; ZHOU Li-ping; YU Yu; LI Zhi-liang

    2007-01-01

    A set of novel structural descriptors (molecular hybridization electronegativity-distance vector, VMEDh) was put forward, and the quantitative structure-activity relationship (QSAR) of a series of 17α-Acetoxyprogesterones (Aps) was investigated. Taking into account the effect of various hybridized orbits on atomic electronegativities, we developed the structure descriptors with amended electronegativities to build a QSAR model. The 10-parameter model based on VMEDh yields a correlation coefficient R=0.972 and standard deviation SD=0.262, which are more desirable than those of the previous molecular electonegativity-distance vector (MEDV-4) (R=0.969, SD=0.275). By stepwise multiple linear regression, several parameters are selected to construct optimal models. The 7-parameter model based on VMEDh has R=0.960 and SD=0.276; its correlation coefficient (RCV) and standard deviation (SDCV) for leave-one-out procedure crossvalidation are respectively RCV=0.890 and SDCV=0.445. The 6-parameter MEDV-4 model has R=0.946, SD=0.304, RCV=0.903 and SDCV=0.406. It is demonstrated that VMEDh has desirable estimation performance and good predictive capability for this series of chemical compounds.

  2. Comparison of quantitative estimation of intracerebral hemorrhage and infarct volumes after thromboembolism in an embolic stroke model

    DEFF Research Database (Denmark)

    Eriksen, Nina; Rasmussen, Rune Skovgaard; Overgaard, Karsten

    2014-01-01

    . AIMS: We evaluated different methods for estimating the volume of infarcts, hemorrhages, after embolic middle cerebral artery occlusion with or without thrombolysis. METHODS: An experimental thromboembolytic rat model was used in this study. The rats underwent surgery and were placed in two groups...... of the infarct and intracerebral hemorrhage. RESULTS: No differences were observed in the infarct volume or amount of bleeding when comparing the three methods of volume estimation. Although semiautomated computer estimation and manual erythrocyte counting provided similar results as the stereological...... measurements, the stereological method was the most efficient and advantageous. CONCLUSIONS: We found that stereology was the superior method for quantification of hemorrhagic volume, especially for rodent petechial bleeding, which is otherwise difficult to measure. Our results suggest the possibility...

  3. Quantitative measurements of trace elements with large activation cross section for concrete materials in Japan

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki, A.; Iida, T.; Moriizumi, J.; Kameyama, T. [Nuclear Engineering, Nagoya Univ., Nagoya, Aichi (Japan); Sakuma, Y. [National Inst. for Fusion Science, Toki, Gifu (Japan); Takada, J.; Yamasaki, K.; Yoshimoto, T. [Kyoto Univ., Kumatori, Osaka (Japan). Research Reactor Inst

    2000-05-01

    It is expected that some nuclear power reactors are decommissioned successively in the near future, since the nuclear power technology matures in Japan. Then, what proportion of the massive concrete waste materials is regarded as radioactive waste materials? It is a serious problem. Suzuki et at., have measured specific activities for concrete materials in Japan. In present study, we have measured quantitatively microelements with large activation cross section in concrete materials, and furnish basic data for the guiding principle of concrete waste materials. We have collected 158 samples of concrete materials in Japan. The samples were ground into pieces of 100 to 200 meshes. The amount of 100 mg in each sample was exposed to neutrons for 1 h in the nuclear reactor of KUR. We have measured radioactive elements of medium life time (La-140, Np-239, etc.) one week later, and radioactive elements of long life time (Co-60, Eu-152, etc.) one month later with Ge detector. Nineteen microelements with large activation cross section were detected. The distribution of Co-60 and Eu-152 concentrations was obtained. The mean concentration of Co-60 is 15.7 ppm, and gabbros, peridotites and basalts have high Co-60 concentrations. The mean value of Eu-152 is 8.8 x 10{sup -1} ppm. Andesites, basalts, sandstones and shales have high Eu-152 concentrations. The activated concentrations for cement depend on the place of the origin. Since the concrete materials with low natural radioactivities as gabbros and peridotites have a tendency to activation, it is necessary to pay attention for concrete materials in nuclear power plant. The natural specific activities included in concrete materials in Japan are 556.2 (16.0-896.0) Bq/kg for K-40, 33.8 (2.96-87.6) Bq/kg for U-238 and 29.1 (2.63-48.4)Bq/kg for Th-232{approx_equal} Ra-228. The quantities of microelements with large activation cross section depend on the species of rocks and the level of the weathering. If we could collect many

  4. Direct estimate of active bacteria: CTC use and limitations

    NARCIS (Netherlands)

    Creach, V.; Baudoux, A.C.; Bertru, G.; Le Rouzic, B.

    2003-01-01

    During the last 10 years, the dye 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) has been used to determine the in situ number of "active" bacteria in different ecosystems. A part of this success is due to a simple protocol, which does not require sophisticated equipment. However, it has not been es

  5. Quantitative and integrative analysis of paracrine hepatocyte activation by nonparenchymal cells upon lipopolysaccharide induction.

    Science.gov (United States)

    Beuke, Katharina; Schildberg, Frank A; Pinna, Federico; Albrecht, Ute; Liebe, Roman; Bissinger, Michaela; Schirmacher, Peter; Dooley, Steven; Bode, Johannes G; Knolle, Percy A; Kummer, Ursula; Breuhahn, Kai; Sahle, Sven

    2017-03-01

    Gut-derived bacterial lipopolysaccharides (LPS) stimulate the secretion of tumour necrosis factor (TNF) from liver macrophages (MCs), liver sinusoidal endothelial cells (LSECs) and hepatic stellate cells (HSCs), which control the acute phase response in hepatocytes through activation of the NF-κB pathway. The individual and cooperative impact of nonparenchymal cells on this clinically relevant response has not been analysed in detail due to technical limitations. To gain an integrative view on this complex inter- and intracellular communication, we combined a multiscale mathematical model with quantitative, time-resolved experimental data of different primary murine liver cell types. We established a computational model for TNF-induced NF-κB signalling in hepatocytes, accurately describing dose-responsiveness for physiologically relevant cytokine concentrations. TNF secretion profiles were quantitatively measured for all nonparenchymal cell types upon LPS stimulation. This novel approach allowed the analysis of individual and collective paracrine TNF-mediated NF-κB induction in hepatocytes, revealing strongest effects of MCs and LSECs on hepatocellular NF-κB signalling. Simulations suggest that both cell types act together to maximize the NF-κB pathway response induced by low LPS concentrations (0.1 and 1 ng/mL). Higher LPS concentrations (≥ 5 ng/mL) induced sufficient TNF levels from MCs or LSECs to induce a strong and nonadjustable pathway response. Importantly, these simulations also revealed that the initial cytokine secretion (1-2 h after stimulation) rather than final TNF level (10 h after stimulation) defines the hepatocellular NF-κB response. This raises the question whether the current experimental standard of single high-dose cytokine administration is suitable to mimic in vivo cytokine exposure.

  6. Development and Validation of RP-HPLC Method for Quantitative Estimation of Vinpocetine in Pure and Pharmaceutical Dosage Forms

    Directory of Open Access Journals (Sweden)

    Subrata Bhadra

    2011-01-01

    Full Text Available A simple, precise, specific, and accurate reversed phase high performance liquid chromatographic (RP-HPLC method was developed and validated for determination of vinpocetine in pure and pharmaceutical dosage forms. The different analytical performance parameters such as linearity, accuracy, specificity, precision, and sensitivity (limit of detection and limit of quantitation were determined according to International Conference on Harmonization ICH Q2 (R1 guidelines. RP-HPLC was conducted on Zorbax C18 (150 mm length × 4.6 mm ID, 5 μm column. The mobile phase was consisting of buffer (containing 1.54% w/v ammonium acetate solution and acetonitrile in the ratio (40 : 60, v/v, and the flow rate was maintained at 1.0 mLmin−1. Vinpocetine was monitored using Agilent 1200 series equipped with photo diode array detector (λ = 280 nm. Linearity was observed in concentration range of 160–240 μgmL−1, and correlation coefficient was found excellent (R2 = 0.999. All the system suitability parameters were found within the range. The proposed method is rapid, cost-effective and can be used as a quality-control tool for routine quantitative analysis of vinpocetine in pure and pharmaceutical dosage forms.

  7. A quantitative real time polymerase chain reaction approach for estimating processed animal proteins in feed: preliminary data

    Directory of Open Access Journals (Sweden)

    Maria Cesarina Abete

    2013-04-01

    Full Text Available Lifting of the ban on the use of processed animal proteins (PAPs from non-ruminants in non-ruminant feed is in the wind, avoiding intraspecies recycling. Discrimination of species will be performed through polymerase chain reaction (PCR, which is at a moment a merely qualitative method. Nevertheless, quantification of PAPs in feed is needed. The aim of this study was to approach the quantitative determination of PAPs in feed through Real Time (RT-PCR technique; three different protocols picked up from the literature were tested. Three different kind of matrices were examined: pure animal meals (bovine, chicken and pork; one feed sample certified by the European reference laboratory on animal proteins (EURL AP in feed spiked with 0.1% bovine meal; and genomic DNAs from bovine, chicken and pork muscles. The limit of detection (LOD of the three protocols was set up. All the results obtained from the three protocols considered failed in the quantification process, most likely due to the uncertain copy numbers of the analytical targets chosen. This preliminary study will allow us to address further investigations, with the purpose of developing a RT-PCR quantitative method.

  8. 3D-quantitative structure-activity relationship study of organophosphate compounds

    Institute of Scientific and Technical Information of China (English)

    ZHAO Jinsong; WANG Bin; DAI Zhaoxia; WANG Xiaodong; KONG Lingren; WANG Liansheng

    2004-01-01

    The biological effects of most organophosphate compounds (OP) are arising by inhibition of the enzyme acetylcholinesterase (AChE). The 3D-quantitative structure-activity relationship (3D-QSAR) on the acute toxicity to housefly (Musca nobulo L.) of 35 dialkyl phenyl phosphate compounds are studied by using comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) methods, and the reaction mechanism between the OP and the AChE are discussed. In contrast to classical QSAR methods, CoMFA and CoMSIA, especially the combination of both approaches, can give more comprehensive and accurate perspectives on the mechanism of the reaction between OP and AChE. The results show that the length of alkyl, and the electronegative of substituent on phenyl of OP have significant effects on the AChE activity, whereas, the hydrophobicity of OP has little influence. The steric and electronic properties of OP have a dominant influence on the reaction between OP and AChE.

  9. Odor-active constituents in fresh pineapple (Ananas comosus [L.] Merr.) by quantitative and sensory evaluation.

    Science.gov (United States)

    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.

  10. Quantitative trait locus analysis of symbiotic nitrogen fixation activity in the model legume Lotus japonicus.

    Science.gov (United States)

    Tominaga, Akiyoshi; Gondo, Takahiro; Akashi, Ryo; Zheng, Shao-Hui; Arima, Susumu; Suzuki, Akihiro

    2012-05-01

    Many legumes form nitrogen-fixing root nodules. An elevation of nitrogen fixation in such legumes would have significant implications for plant growth and biomass production in agriculture. To identify the genetic basis for the regulation of nitrogen fixation, quantitative trait locus (QTL) analysis was conducted with recombinant inbred lines derived from the cross Miyakojima MG-20 × Gifu B-129 in the model legume Lotus japonicus. This population was inoculated with Mesorhizobium loti MAFF303099 and grown for 14 days in pods containing vermiculite. Phenotypic data were collected for acetylene reduction activity (ARA) per plant (ARA/P), ARA per nodule weight (ARA/NW), ARA per nodule number (ARA/NN), NN per plant, NW per plant, stem length (SL), SL without inoculation (SLbac-), shoot dry weight without inoculation (SWbac-), root length without inoculation (RLbac-), and root dry weight (RWbac-), and finally 34 QTLs were identified. ARA/P, ARA/NN, NW, and SL showed strong correlations and QTL co-localization, suggesting that several plant characteristics important for symbiotic nitrogen fixation are controlled by the same locus. QTLs for ARA/P, ARA/NN, NW, and SL, co-localized around marker TM0832 on chromosome 4, were also co-localized with previously reported QTLs for seed mass. This is the first report of QTL analysis for symbiotic nitrogen fixation activity traits.

  11. A Caco-2 cell-based quantitative antioxidant activity assay for antioxidants.

    Science.gov (United States)

    Wan, Hongxia; Liu, Dong; Yu, Xiangying; Sun, Haiyan; Li, Yan

    2015-05-15

    A Caco-2 cell-based antioxidant activity (CAA) assay for quantitative evaluation of antioxidants was developed by optimizing seeding density and culture time of Caco-2 cells, incubation time and concentration of fluorescent probe (2',7'-dichlorofluorescin diacetate, DCFH-DA), incubation way and incubation time of antioxidants (pure phytochemicals) and DCFH-DA with cells, and detection time of fluorescence. Results showed that the CAA assay was of good reproducibility and could be used to evaluate the antioxidant activity of antioxidants at the following conditions: seeding density of 5 × 10(4)/well, cell culture time of 24h, co-incubation of 60 μM DCFH-DA and pure phytochemicals with Caco-2 cells for 20 min and fluorescence recorded for 90 min. Additionally, a significant correlation was observed between CAA values and rat plasma ORAC values following the intake of antioxidants for selected pure phytochemicals (R(2) = 0.815, p < 0.01), demonstrating the good biological relevance of CAA assay. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. A Concurrent Mixed Methods Approach to Examining the Quantitative and Qualitative Meaningfulness of Absolute Magnitude Estimation Scales in Survey Research

    Science.gov (United States)

    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…

  13. A Concurrent Mixed Methods Approach to Examining the Quantitative and Qualitative Meaningfulness of Absolute Magnitude Estimation Scales in Survey Research

    Science.gov (United States)

    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…

  14. A study on deep geological environment for the radwaste disposal - Estimation of roughness for the quantitative analysis of fracture transmissivity

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jung Yul; Kim, J. Y.; Kim, Y. S.; Hyun, H. J. [Korea Institute of Geology, Mining and Materials, Taejon (Korea)

    2000-03-01

    Estimation of fracture roughness-as one of the basic hydraulic fracture parameters - is very important in assessing ground water flow described by using discrete fracture network modeling. Former manual estimation of the roughness for each fracture surface of drill cores is above all a tedious, time-consuming work and will often cause some ambiguities of roughness interpretation partly due to the subjective judgements of observers, and partly due to the measuring procedure itself. However, recently, indebt to the highly reliable Televiewer data for the fracture discrimination, it has led to a guess to develop a relationship between the traditional roughness method based on a linear profiles and the method from the Televiewer image based on a ellipsoidal profile. Hence, the aim of this work is to develop an automatic evaluation algorithm for measuring the roughness from the Televiewer images. A highly reliable software named 'RAF' has been developed and realized to the extent that its utility merits. In the developing procedure, various problems - such as the examination of a new base line(ellipsoidal) for measuring the unevenness of fracture, the elimination of overlapping fracture signatures or noise, the wavelet estimation according to the type of fractures and the digitalization of roughness etc. - were considered. With these consideration in mind, the newly devised algorithm for the estimation of roughness curves showed a great potential not only for avoiding ambiguities of roughness interpretation but also for the judgement of roughness classification. 12 refs., 23 figs. (Author)

  15. Stereological estimates of nuclear volume and other quantitative variables in supratentorial brain tumors. Practical technique and use in prognostic evaluation

    DEFF Research Database (Denmark)

    Sørensen, Flemming Brandt; Braendgaard, H; Chistiansen, A O

    1991-01-01

    the practical technique. The continuous variables were correlated with the subjective, qualitative WHO classification of brain tumors, and the prognostic value of the parameters was assessed. Well differentiated astrocytomas (n = 14) had smaller estimates of the volume-weighted mean nuclear volume and mean...

  16. A meta-analysis of neuroimaging studies on divergent thinking using activation likelihood estimation.

    Science.gov (United States)

    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). © 2015 Wiley Periodicals, Inc.

  17. Methodology for estimating dietary data from the semi-quantitative food frequency questionnaire of the Mexican National Health and Nutrition Survey 2012

    Directory of Open Access Journals (Sweden)

    Ivonne Ramírez-Silva

    2016-12-01

    Full Text Available Objective. To describe the methodology used to clean up and estimate dietary intake (DI data from the Semi-Quantitative Food Frequency Questionnaire (SFFQ of the Mexican National Health and Nutrition Survey 2012. Materials and methods. DI was collected through a shortterm SFFQ regarding 140 foods (from October 2011 to May 2012. Energy and nutrient intake was calculated accordingto a nutrient database constructed specifically for the SFFQ. Results. A total of 133 nutrients including energy and fiber were generated from SFFQ data. Between 4.8 and 9.6% of the survey sample was excluded as a result of the cleaning process. Valid DI data were obtained regarding energy and nutrients consumed by 1 212 pre-school children, 1 323 school children, 1 961 adolescents, 2 027 adults and 526 older adults. Conclusions. We documented the methodology used to clean up and estimate DI from the SFFQ used in national dietary assessments in Mexico.

  18. 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

    Science.gov (United States)

    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

  19. Quantitative estimation of climatic parameters from vegetation data in North America by the mutual climatic range technique

    Science.gov (United States)

    Anderson, Katherine H.; Bartlein, Patrick J.; Strickland, Laura E.; Pelltier, Richard T.; Thompson, Robert S.; Shafer, Sarah L.

    2012-01-01

    The mutual climatic range (MCR) technique is perhaps the most widely used method for estimating past climatic parameters from fossil assemblages, largely because it can be conducted on a simple list of the taxa present in an assemblage. When applied to plant macrofossil data, this unweighted approach (MCRun) will frequently identify a large range for a given climatic parameter where the species in an assemblage can theoretically live together. To narrow this range, we devised a new weighted approach (MCRwt) that employs information from the modern relations between climatic parameters and plant distributions to lessen the influence of the "tails" of the distributions of the climatic data associated with the taxa in an assemblage. To assess the performance of the MCR approaches, we applied them to a set of modern climatic data and plant distributions on a 25-km grid for North America, and compared observed and estimated climatic values for each grid point. In general, MCRwt was superior to MCRun in providing smaller anomalies, less bias, and better correlations between observed and estimated values. However, by the same measures, the results of Modern Analog Technique (MAT) approaches were superior to MCRwt. Although this might be reason to favor MAT approaches, they are based on assumptions that may not be valid for paleoclimatic reconstructions, including that: 1) the absence of a taxon from a fossil sample is meaningful, 2) plant associations were largely unaffected by past changes in either levels of atmospheric carbon dioxide or in the seasonal distributions of solar radiation, and 3) plant associations of the past are adequately represented on the modern landscape. To illustrate the application of these MCR and MAT approaches to paleoclimatic reconstructions, we applied them to a Pleistocene paleobotanical assemblage from the western United States. From our examinations of the estimates of modern and past climates from vegetation assemblages, we conclude that

  20. Quantitative assessment of swallowing activity by MMG measurement with PVDF film.

    Science.gov (United States)

    Takuya, Hashimoto; Keita, Tsukagoshi; Takuji, Koike

    2017-07-01

    Difficulty of swallowing, called dysphagia, leads to aspiration pneumonia which is particularly a big health concern in aging societies. Therefore, prevention and treatment of dysphagia would contribute to extending healthy-life and QOL of elderly people and decreasing healthcare cost. Robotics technologies are expected as one of the effective methods to solve the problem in terms of detecting malfunction in swallowing and recovering swallowing function. The aim of this study is to investigate muscle activity during normal swallowing using mechanomyography (MMG) with PolyVinylidene DiFluoride (PVDF) film which is a ferroelectrics polymer. Measurement of MMG signal during voluntary isometric contraction of the biceps brachii muscle was conducted to confirm whether PVDF film can detect MMG signal. In the experiment, surface electromyography (sEMG) was also measured as a reference to estimate muscle activity for comparison. Then, activities of swallowing muscles during normal swallowing with different volume of bolus were measured using MMG signal. As the result, it was confirmed that swallowing activity can be quantified by the detected MMG signal from different region of neck.

  1. Quantitative estimation of granitoid composition from thermal infrared multispectral scanner (TIMS) data, Desolation Wilderness, northern Sierra Nevada, California

    Science.gov (United States)

    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.

  2. Impedance rheoplethysmography. The role of estimation of vasodilatory activity.

    Science.gov (United States)

    Demenge, P; Silice, C; Lebas, J F; Piquard, J F; Carraz, G

    1979-01-01

    The activity of a number of vasodilatory drugs was studied, with the help of impedance rheoplethysmography, on the vascular bed of the hind limb of anaesthetized rabbits. The vasodilators under study induce changes in rheoplethysmogram to a more or less important degree. The results were compared with those obtained with electromagnetic flowmetry. This method seems to be useful in the study of vasodilators because it allows to measure their effects and the duration thereof in a non-aggressive way. This method using flowmetry, allows to study in an analytical way those substances' effects on artery, vein and also capillary.

  3. A quantitative structure–activity relationship (QSAR) study of peptide drugs based on a new descriptor of amino acids

    OpenAIRE

    Tong Jian-Bo; Chang Jia; Liu Shu-Ling; Bai Min

    2015-01-01

    Quantitative structure-activity relationships (QSAR) approach is used for finding the relationship between molecular structures and the activity of peptide drugs. In this work, stepwise multiple regression, was employed to select optimal subset of descriptors that have significant contribution to the drug activity of 21 oxytocin analogues, 48 bitter tasting threshold, and 58 angiotensin-converting enzyme inhibitors. A new set of descriptor, SVWGM, was used ...

  4. Hawaii Clean Energy Initiative (HCEI) Scenario Analysis: Quantitative Estimates Used to Facilitate Working Group Discussions (2008-2010)

    Energy Technology Data Exchange (ETDEWEB)

    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.

  5. Quantitative estimation of insulin sensitivity in type 1 diabetic subjects wearing a sensor-augmented insulin pump.

    Science.gov (United States)

    Schiavon, Michele; Dalla Man, Chiara; Kudva, Yogish C; Basu, Ananda; Cobelli, Claudio

    2014-01-01

    The goal was to develop a new index of insulin sensitivity in patients with type 1 diabetes estimated from continuous glucose monitoring (CGM) and subcutaneous insulin delivery data under carefully controlled conditions. The database consists of 12 subjects with type 1 diabetes, studied during breakfast, lunch, and dinner, in a clinical research unit, wearing both subcutaneous insulin pump and CGM device. Frequent blood samples were drawn for measurements of plasma glucose and insulin concentrations in order to estimate insulin sensitivity with the oral minimal model (SI(MM)). The new index of insulin sensitivity (SI(SP)) was calculated with a simple algebraic formula for each meal, using only CGM and insulin pump data and compared with SI(MM). SI(SP) was well correlated with SI(MM) (r = 0.825; P insulin sensitivity in subjects with type 1 diabetes on sensor-augmented insulin pump therapy has been presented. This new index correlates well with the reference oral minimal model estimate of insulin sensitivity. The knowledge of patient-specific insulin sensitivity and its diurnal variation can help in optimizing insulin therapy in type 1 diabetes and could also inform next-generation closed-loop control systems.

  6. Quantitative estimation of farmland soil loss by wind-erosion using improved particle-size distribution comparison method (IPSDC)

    Science.gov (United States)

    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. Methodology for a bounding estimate of activation source-term.

    Science.gov (United States)

    Culp, Todd

    2013-02-01

    Sandia National Laboratories' Z-Machine is the world's most powerful electrical device, and experiments have been conducted that make it the world's most powerful radiation source. Because Z-Machine is used for research, an assortment of materials can be placed into the machine; these materials can be subjected to a range of nuclear reactions, producing an assortment of activation products. A methodology was developed to provide a systematic approach to evaluate different materials to be introduced into the machine as wire arrays. This methodology is based on experiment specific characteristics, physical characteristics of specific radionuclides, and experience with Z-Machine. This provides a starting point for bounding calculations of radionuclide source-term that can be used for work planning, development of work controls, and evaluating materials for introduction into the machine.

  8. Development of response surface methodology for optimization of extraction parameters and quantitative estimation of embelin from Embelia ribes Burm by high performance liquid chromatography

    Science.gov (United States)

    Alam, Md. Shamsir; Damanhouri, Zoheir A.; Ahmad, Aftab; Abidin, Lubna; Amir, Mohd; Aqil, Mohd; Khan, Shah Alam; Mujeeb, Mohd

    2015-01-01

    Background: Embelia ribes Burm is widely used medicinal plant for the treatment of different types of disorders in the Indian traditional systems of medicine. Objective: The present work was aimed to optimize the extraction parameters of embelin from E. ribes fruits and also to quantify embelin content in different extracts of the plant. Materials and Methods: Optimization of extraction parameters such as solvent: drug ratio, temperature and time were carried out by response surface methodology (RSM). Quantitative estimation of embelin in different extracts of E. ribes fruits was done through high performance liquid chromatography. Results: The optimal conditions determined for extraction of embelin through RSM were; extraction time (27.50 min), extraction temperature 45°C and solvent: drug ratio (8:1). Under the optimized conditions, the embelin yield (32.71%) was equitable to the expected yield (31.07%, P > 0.05). These results showed that the developed model is satisfactory and suitable for the extraction process of embelin. The analysis of variance showed a high goodness of model fit and the accomplishment of the RSM method for improving embelin extraction from the fruits of E. ribes. Conclusion: It is concluded that this may be a useful method for the extraction and quantitative estimation of embelin from the fruits of E. ribes. PMID:26109763

  9. Development of response surface methodology for optimization of extraction parameters and quantitative estimation of embelin from Embelia ribes Burm by high performance liquid chromatography

    Directory of Open Access Journals (Sweden)

    Md. Shamsir Alam

    2015-01-01

    Full Text Available Background: Embelia ribes Burm is widely used medicinal plant for the treatment of different types of disorders in the Indian traditional systems of medicine. Objective: The present work was aimed to optimize the extraction parameters of embelin from E. ribes fruits and also to quantify embelin content in different extracts of the plant. Materials and Methods: Optimization of extraction parameters such as solvent: drug ratio, temperature and time were carried out by response surface methodology (RSM. Quantitative estimation of embelin in different extracts of E. ribes fruits was done through high performance liquid chromatography. Results: The optimal conditions determined for extraction of embelin through RSM were; extraction time (27.50 min, extraction temperature 45°C and solvent: drug ratio (8:1. Under the optimized conditions, the embelin yield (32.71% was equitable to the expected yield (31.07%, P > 0.05. These results showed that the developed model is satisfactory and suitable for the extraction process of embelin. The analysis of variance showed a high goodness of model fit and the accomplishment of the RSM method for improving embelin extraction from the fruits of E. ribes. Conclusion: It is concluded that this may be a useful method for the extraction and quantitative estimation of embelin from the fruits of E. ribes.

  10. Quantitative comparison of suitability of various beams for range monitoring with induced beta+ activity in hadron therapy.

    Science.gov (United States)

    Inaniwa, Taku; Tomitani, Takehiro; Kohno, Toshiyuki; Kanai, Tatsuaki

    2005-03-21

    In radiation therapy with hadron beams, it is important to evaluate the range of incident ions and the deposited dose distribution in a patient body for the effective utilization of such properties as the dose concentration and the biological effect around the Bragg peak. However, there is some ambiguity in determining this range because of a conversion error from the x-ray CT number to the charged particle range. This is because the CT number is related to x-ray absorption coefficients, while the ion range is determined by the electron density of the substance. Using positron emitters produced in the patient body through fragmentation reactions during the irradiation has been proposed to overcome this problem. The activity distribution in the patient body can be deduced by detecting pairs of annihilation gamma rays emitted from the positron emitters, and information about the range of incident ions can be obtained. In this paper, we propose a quantitative comparison method to evaluate the mean range of incident ions and monitor the activity distribution related to the deposited dose distribution. The effectiveness of the method was demonstrated by evaluating the range of incident ions using the maximum likelihood estimation (MLE) method and Fisher's information was calculated under realistic conditions for irradiations with several kinds of ions. From the calculated Fisher's information, we compared the relative advantages of initial beams to determine the range of incident ions. The (16)O irradiation gave the most information among the stable heavy ions when we measured the induced activity for 500 s and 60 s just after the irradiation. Therefore, under these conditions, we concluded that the (16)O beam was the optimum beam to monitor the activity distribution and to evaluate the range. On the other hand, if the positron emitters were injected directly as a therapeutic beam, the (15)O irradiation gave the most information. Although the relative advantages of

  11. A semianalytical algorithm for quantitatively estimating sediment and atmospheric deposition flux from MODIS-derived sea ice albedo in the Bohai Sea, China

    Science.gov (United States)

    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.

  12. On Using WWLLN Observations as Starting Information for the Quantitative Schumann Resonance Monitoring of Global Lightning Activity

    Science.gov (United States)

    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.

  13. Quantitative structure-activity relationships for nasal pungency thresholds of volatile organic compounds.

    Science.gov (United States)

    Hau, K M; Connell, D W; Richardson, B J

    1999-01-01

    A model was developed for describing the triggering of nasal pungency in humans, based on the partition of volatile organic compounds (VOCs) between the air phase and the biophase. Two partition parameters are used in the model: the water-air partition coefficient and the octanol-water partition coefficient. The model was validated using data from the literature, principally on alcohols, acetates and ketones. The model suggests that all test compounds, regardless of their chemical functional groups, bind to a common receptor site within the hydrophobic interior of the bilayer membrane of the trigeminal nerve endings. There is probably only a slight, non-specific interaction between the VOC molecule and the receptor molecule, whereas this type of non-specific interaction for the detection of odor is much stronger. In practical terms, the suggestion that all VOCs share a common irritation receptor site implies that nasal-pungency thresholds of individual VOCs may be additive. Quantitative structure-activity relationships (QSARs) for nasal-pungency thresholds were also developed from the model, which can be used to predict nasal-pungency thresholds of common VOCs. Although the present model does not offer additional precision over that of M.H. Abraham et al., 1996, Fundam. Appl. Toxicol. 31, 71-76, it requires fewer descriptors and offers a physiological basis to the QSAR. Another advantage of the present model is that it also provides a basis for comparison between the olfactory process and nasal pungency.

  14. Predicting Flash Point of Organosilicon Compounds Using Quantitative Structure Activity Relationship Approach

    Directory of Open Access Journals (Sweden)

    Chen-Peng Chen

    2014-01-01

    Full Text Available The flash point (FP of a compound is the primary property used in the assessment of fire hazards for flammable liquids and is amongst the crucial information that people handling flammable liquids must possess as far as industrial safety is concerned. In this work, the FPs of 236 organosilicon compounds were collected and used to construct a quantitative structure activity relationship (QSAR model for predicting their FPs. The CODESSA PRO software was adopted to calculate the required molecular descriptors, and 350 molecular descriptors were developed for each compound. A modified stepwise regression algorithm was applied to choose descriptors that were highly correlated with the FP of organosilicon compounds. The proposed model was a linear regression model consisting of six descriptors. This 6-descriptor model gave an R2 value of 0.9174, QLOO2 value of 0.9106, and Q2 value of 0.8989. The average fitting error and the average predictive error were found to be of 10.34 K and 11.22 K, respectively, and the average fitting error in percentage and the average predictive error in percentage were found to be of 3.30 and 3.60%, respectively. Compared with the known reproducibility of FP measurement using standard test method, these predicted results were of a satisfactory precision.

  15. Investigation and prediction of protein precipitation by polyethylene glycol using quantitative structure-activity relationship models.

    Science.gov (United States)

    Hämmerling, Frank; Ladd Effio, Christopher; Andris, Sebastian; Kittelmann, Jörg; Hubbuch, Jürgen

    2017-01-10

    Precipitation of proteins is considered to be an effective purification method for proteins and has proven its potential to replace costly chromatography processes. Besides salts and polyelectrolytes, polymers, such as polyethylene glycol (PEG), are commonly used for precipitation applications under mild conditions. Process development, however, for protein precipitation steps still is based mainly on heuristic approaches and high-throughput experimentation due to a lack of understanding of the underlying mechanisms. In this work we apply quantitative structure-activity relationships (QSARs) to model two parameters, the discontinuity point m* and the β-value, that describe the complete precipitation curve of a protein under defined conditions. The generated QSAR models are sensitive to the protein type, pH, and ionic strength. It was found that the discontinuity point m* is mainly dependent on protein molecular structure properties and electrostatic surface properties, whereas the β-value is influenced by the variance in electrostatics and hydrophobicity on the protein surface. The models for m* and the β-value exhibit a good correlation between observed and predicted data with a coefficient of determination of R(2)≥0.90 and, hence, are able to accurately predict precipitation curves for proteins. The predictive capabilities were demonstrated for a set of combinations of protein type, pH, and ionic strength not included in the generation of the models and good agreement between predicted and experimental data was achieved.

  16. Quantitative structure-activity relationship and prediction of mixture toxicity of alkanols

    Institute of Scientific and Technical Information of China (English)

    WANG Bin; YU Gang; ZHANG Zulin; HU Hongying; WANG Liansheng

    2006-01-01

    Alkanols, which are narcotic compounds,were studied. The acute toxicities (15min-EG50) of 15alkanols, which have a large span of hydrophobicity,to Photobacterium phosphoreum were measured.Quantitative structure-activity relationship (QSAR)analysis of single toxicity of alkanols was conducted by using octanol-water partition coefficient (logKow).The polynomial expression was used instead of linear equation to develop QSAR model, and a QSAR model with a good predictive potential was achieved.Furthermore, the mixture toxicity of alkanols was studied. In order to predict joint toxicity of mixtures that contain very hydrophobic alkanols, the adjustment of octanol-water partition coefficient was performed, considering the influence of volume effect.And equivalent octanol-water partition coefficient was introduced. The QSAR model of mixture toxicity was developed by using equivalent mixture octanol-water partition coefficient. The result showed that even a linear model could predict mixture toxicity well by using equivalent mixture octanol-water partition coefficient.

  17. Holographic quantitative structure-activity relationship for prediction of the toxicity of polybrominated diphenyl ether congeners

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Polybrominated diphenyl ether congeners (PBDEs) might activate the AhR (aromatic hydrocarbon receptor) signal transduction,and thus might have an adverse effect on the health of humans and wildlife. Because of the limited experimental data,it is important and necessary to develop structure-based models for prediction of the toxicity of the compounds. In this study,a new molecular structure representation,molecular hologram,was employed to investigate the quantitative relationship between toxicity and molecular structures for 18 PBDEs. The model with the significant correlation and robustness (r2 = 0.991,q2LOO = 0.917) was developed. To verify the robustness and prediction capacity of the derived model,14 PBDEs were randomly selected from the database as the training set,while the rest were used as the test set. The results generated under the same modeling conditions as the optimal model are as follows:r2 = 0.988,q2LOO = 0.598,r2pred = 0.955,and RMSE (root-mean-square of errors) = 0.155,suggesting the excellent ability of the derived model to predict the toxicity of PBDEs. Furthermore,the structural features and molecular mechanism related to the toxicity of PBDEs were explored using HQSAR color coding.

  18. Advances in quantitative structure-activity relationship models of anti-Alzheimer's agents.

    Science.gov (United States)

    Ambure, Pravin; Roy, Kunal

    2014-06-01

    Alzheimer's disease (AD) is one of the lethal diseases, mainly affecting older people. The unclear root cause and involvement of various enzymes in the pathological conditions confirm the complexity of the disease. Quantitative structure-activity relationship (QSAR) techniques are of great significance in the design of drugs against AD. In the present review, the authors provide a basic background about AD and QSAR techniques. Furthermore, they review the various QSAR studies reported against various targets of AD. The information provided for each QSAR study includes chemical scaffold and target enzyme under study, applied QSAR technique and outcomes of the respective study. In silico techniques like QSAR hold great potential in designing leads against a complex disease like AD. In combination with other in silico techniques, QSAR can provide more useful and rational insight to facilitate the discovery of novel compounds. Only few QSAR studies on imaging agents have been reported; hence, more QSAR studies are recommended to explore the biomarker or imaging agents for improving diagnosis. Again, for proper symptomatic treatment, multi-target drugs acting on more than one target are required. Hence, more multi-target QSAR studies are recommended in future to achieve this goal.

  19. Blood-brain barrier permeability mechanisms in view of quantitative structure-activity relationships (QSAR).

    Science.gov (United States)

    Bujak, Renata; Struck-Lewicka, Wiktoria; Kaliszan, Michał; Kaliszan, Roman; Markuszewski, Michał J

    2015-04-10

    The goal of the present paper was to develop a quantitative structure-activity relationship (QSAR) method using a simple statistical approach, such as multiple linear regression (MLR) for predicting the blood-brain barrier (BBB) permeability of chemical compounds. The "best" MLR models, comprised logP and either molecular mass (M) or isolated atomic energy (E(isol)), tested on a structurally diverse set of 66 compounds, is characterized the by correlation coefficients (R) around 0.8. The obtained models were validated using leave-one-out (LOO) cross-validation technique and the correlation coefficient of leave-one-out- R(LOO)(2) (Q(2)) was at least 0.6. Analysis of a case from legal medicine demonstrated informative value of our QSAR model. To best authors' knowledge the present study is a first application of the developed QSAR models of BBB permeability to case from the legal medicine. Our data indicate that molecular energy-related descriptors, in combination with the well-known descriptors of lipophilicity may have a supportive value in predicting blood-brain distribution, which is of utmost importance in drug development and toxicological studies.

  20. The uridine diphosphate glucuronosyltransferases: quantitative structure-activity relationships for hydroxyl polychlorinated biphenyl substrates

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Degao [Dalian University of Technology, Department of Environmental Science and Technology, Dalian (China)

    2005-10-01

    Quantitative structure-activity relationships (QSARs), which relate the glucuronidation of hydroxyl polychlorinated biphenyls (OH-PCBs) - catalyzed by the uridine diphosphate glucuronosyltransferases (UGTs) - to their physicochemical properties and molecular structural parameters, can be used to predict the rate constants and interpret the mechanism of glucuronidation. In this study, QSARs have been developed that use 23 semi-empirical calculated quantum chemical descriptors to predict the logarithms of the constants 1/K{sub m} and V{sub max}, related to enzyme kinetics. A partial least squares regression method was used to select the optimal set of descriptors to minimize the multicollinearity between the descriptors, as well as to maximize the cross-validated coefficient (Q{sup 2} {sub cum}) values. The key descriptors affecting log(1/K{sub m}) were E{sub lumo}- E{sub homo} (the energy gap between the lowest unoccupied molecular orbital and the highest occupied molecular orbital) and q{sub C}{sup -} (the largest negative net atomic charge on a carbon atom), while the key descriptors affecting log V{sub max} were the polarizability {alpha}, the Connolly solvent-excluded volume (CSEV), and logP (the logarithm of the partition coefficient for octanol/water). From the results obtained it can be concluded that hydrophobic and electronic aspects of OH-PCBs are important in the glucuronidation of OH-PCBs. (orig.)

  1. Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries.

    Science.gov (United States)

    Bush, Stephen J; McCulloch, Mary E B; Summers, Kim M; Hume, David A; Clark, Emily L

    2017-06-13

    The availability of fast alignment-free algorithms has greatly reduced the computational burden of RNA-seq processing, especially for relatively poorly assembled genomes. Using these approaches, previous RNA-seq datasets could potentially be processed and integrated with newly sequenced libraries. Confounding factors in such integration include sequencing depth and methods of RNA extraction and selection. Different selection methods (typically, either polyA-selection or rRNA-depletion) omit different RNAs, resulting in different fractions of the transcriptome being sequenced. In particular, rRNA-depleted libraries sample a broader fraction of the transcriptome than polyA-selected libraries. This study aimed to develop a systematic means of accounting for library type that allows data from these two methods to be compared. The method was developed by comparing two RNA-seq datasets from ovine macrophages, identical except for RNA selection method. Gene-level expression estimates were obtained using a two-part process centred on the high-speed transcript quantification tool Kallisto. Firstly, a set of reference transcripts was defined that constitute a standardised RNA space, with expression from both datasets quantified against it. Secondly, a simple ratio-based correction was applied to the rRNA-depleted estimates. The outcome is an almost perfect correlation between gene expression estimates, independent of library type and across the full range of levels of expression. A combination of reference transcriptome filtering and a ratio-based correction can create equivalent expression profiles from both polyA-selected and rRNA-depleted libraries. This approach will allow meta-analysis and integration of existing RNA-seq data into transcriptional atlas projects.

  2. An operational weather radar-based Quantitative Precipitation Estimation and its application in catchment water resources modeling

    DEFF Research Database (Denmark)

    He, Xin; Vejen, Flemming; Stisen, Simon

    2011-01-01

    of precipitation compared with rain-gauge-based methods, thus providing the basis for better water resources assessments. The radar QPE algorithm called ARNE is a distance-dependent areal estimation method that merges radar data with ground surface observations. The method was applied to the Skjern River catchment...... reliable simulations of stream flow and water balance. The potential of using radar-based precipitation was found to be especially high at a smaller scale, where the impact of spatial resolution was evident from the stream discharge results. Also, groundwater recharge was shown to be sensitive...

  3. Quantitative Estimation of Coastal Changes along Selected Locations of Karnataka, India: A GIS and Remote Sensing Approach

    Digital Repository Service at National Institute of Oceanography (India)

    Vinayaraj, P.; Johnson, G.; Dora, G.U.; Philip, C.S.; SanilKumar, V.; Gowthaman, R.

    station are presented by overlaying to- gether. Quantification of erosion/accretion rate is done by digitization as polygon features using ArcGIS. Coastal process are not uniform with respect to time and it is difficult to compare two scenes taken... at differ- ent time because of the non-uniform tides of coastal area i.e., if it is low tide in one scene, it may be high tide in other one. So there is chance of error in estimation of erosion/accretion [10]. For minimizing the error, the data during...

  4. Quantitative MRI reveals decelerated fatty infiltration in muscles of active FSHD patients.

    Science.gov (United States)

    Janssen, Barbara; Voet, Nicoline; Geurts, Alexander; van Engelen, Baziel; Heerschap, Arend

    2016-05-03

    To investigate the effects of aerobic exercise training (AET) and cognitive-behavioral therapy (CBT), directed towards an increase in daily physical activity, on the progression of fatty infiltration and edema in skeletal muscles of patients with facioscapulohumeral muscular dystrophy (FSHD) type 1 by T2 MRI. Quantitative T2 MRI (qT2 MRI) and fat-suppressed T2 MRI of the thigh were performed at 3T on 31 patients, 13 of whom received usual care (UC), 9 AET, and 9 CBT. Muscle-specific fat fractions (%), derived from qT2 MRI, were recorded pretreatment and posttreatment. Intervention effects were analyzed by comparing fat fraction progression rates of the UC with the treated groups using Mann-Whitney tests, and intermuscle differences by a linear mixed model. Edematous hyperintense lesions were identified on the fat-suppressed T2 MRI. The intraclass correlation coefficient for reproducibility of qT2 MRI fat assessment was 0.99. In the UC group, the fat fraction increased by 6.7/year (95% confidence interval [CI] 4.3 to 9.1). This rate decreased to 2.9/year (95% CI 0.7 to 5.2) in the AET (p = 0.03) and 1.7/year (95% CI -0.2 to 3.6) in the CBT group (p = 0.00015). The treatment effect differed among individual muscles. Fewer new edematous lesions occurred after therapy. Fat fraction derived from qT2 MRI is a reproducible and sensitive biomarker to monitor the effects of increased physical activity in individual muscles. This biomarker reports a favorable effect of AET and CBT on the rate of muscular deterioration in FSHD as reflected in decelerated fat replacement. This study provides Class II evidence that for patients with FSHD type 1, both AET and CBT decrease the rate of fatty infiltration in muscles. © 2016 American Academy of Neurology.

  5. Quantitative evaluation of leg lymphedema by MR imaging. Estimation of therapeutic effect by intra-arterial injection of lymphocytes

    Energy Technology Data Exchange (ETDEWEB)

    Makimoto, Yumi; Harada, Masafumi; Matsuzaki, Kenji; Hayashi, Yoshinori; Nishitani, Hiromu; Yoshizumi, Masanori; Yoshida, Osamu; Katoh, Itsuo [Tokushima Univ. (Japan). School of Medicine

    1994-12-01

    The purpose of this study was to obtain characteristic findings of lymphedema and reactions after intra-arterial lymphocytes injection therapy by MRI and to evaluate quantitatively effect of intra-arterial lymphocytes injection. Five patients were treated by several intra-arterial lymphocytes injections. We measured T{sub 2} value on edematous tissue using triple echo sequence and shot TI IR (STIR) images to assess the extent of lymphedema. MRI was measured before and after each intra-arterial lymphocytes injection. Mean T{sub 2} and standard deviation (SD) of T{sub 2} distribution were obtained from T{sub 2}-calculated images. Characteristic findings of lymphedema were the thickening of subcutaneous, meshed pattern of fluid, thickening of skin, and fluid on the fascia. After therapy, thickness of subcutaneous tissue and meshed pattern were greatly decreased, but thickening of skin and fluid on the fascia still remained. Mean T{sub 2} and SD of T{sub 2} in edematous tissue were much higher than those of normal tissue. Both of them decreased extremely after therapy on improved cases but did not change on less effective cases. STIR could differentiate water from adipose tissue and clearly indicated the distribution of water. Mean T{sub 2} and SD of T{sub 2} distribution were useful to indicate evaluation of lymphedema and assessment of therapy. (author).

  6. Modeling number of bacteria per food unit in comparison to bacterial concentration in quantitative risk assessment: impact on risk estimates.

    Science.gov (United States)

    Pouillot, Régis; Chen, Yuhuan; Hoelzer, Karin

    2015-02-01

    When developing quantitative risk assessment models, a fundamental consideration for risk assessors is to decide whether to evaluate changes in bacterial levels in terms of concentrations or in terms of bacterial numbers. Although modeling bacteria in terms of integer numbers may be regarded as a more intuitive and rigorous choice, modeling bacterial concentrations is more popular as it is generally less mathematically complex. We tested three different modeling approaches in a simulation study. The first approach considered bacterial concentrations; the second considered the number of bacteria in contaminated units, and the third considered the expected number of bacteria in contaminated units. Simulation results indicate that modeling concentrations tends to overestimate risk compared to modeling the number of bacteria. A sensitivity analysis using a regression tree suggests that processes which include drastic scenarios consisting of combinations of large bacterial inactivation followed by large bacterial growth frequently lead to a >10-fold overestimation of the average risk when modeling concentrations as opposed to bacterial numbers. Alternatively, the approach of modeling the expected number of bacteria in positive units generates results similar to the second method and is easier to use, thus potentially representing a promising compromise.

  7. Estimation of age at death based on quantitation of the 4977-bp deletion of human mitochondrial DNA in skeletal muscle.

    Science.gov (United States)

    Meissner, C; von Wurmb, N; Schimansky, B; Oehmichen, M

    1999-11-01

    The 4977-bp deletion in human mitochondrial DNA (mtDNA) is known to accumulate in various tissues with age. Since this deletion in mtDNA correlates closest with age in muscle tissue, iliopsoas muscle tissue was taken at autopsy from 50 persons aged 24-97 years to determine whether age at death can be estimated based on the amount of the 4977-bp deletion in skeletal muscle. Total DNA (nuclear and mtDNA) was extracted from 100 mg tissue and the 4977-bp deletion quantified using a kinetic polymerase chain reaction (PCR) followed by visualization of the products on silver stained polyacrylamide gels. The amount of the 4977-bp deletion of mtDNA ranged from 0.00049% to 0.14% depending on age, with a correlation coefficient of r = 0.83 (P = 0.0001). In forensic practice this method can aid in the estimation of age at death with a relatively wide confidence interval, thus enabling a discrimination between young and elderly persons in the identification of human remains based solely on skeletal muscle.

  8. Non-Exercise Estimation of VO[subscript 2]max Using the International Physical Activity Questionnaire

    Science.gov (United States)

    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…

  9. Non-Exercise Estimation of VO[subscript 2]max Using the International Physical Activity Questionnaire

    Science.gov (United States)

    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…

  10. Secondary dentine as a sole parameter for age estimation: Comparison and reliability of qualitative and quantitative methods among North Western adult Indians

    Directory of Open Access Journals (Sweden)

    Jasbir Arora

    2016-06-01

    Full Text Available The indestructible nature of teeth against most of the environmental abuses makes its use in disaster victim identification (DVI. The present study has been undertaken to examine the reliability of Gustafson’s qualitative method and Kedici’s quantitative method of measuring secondary dentine for age estimation among North Western adult Indians. 196 (M = 85; F = 111 single rooted teeth were collected from the Department of Oral Health Sciences, PGIMER, Chandigarh. Ground sections were prepared and the amount of secondary dentine formed was scored qualitatively according to Gustafson’s (0–3 scoring system (method 1 and quantitatively following Kedici’s micrometric measurement method (method 2. Out of 196 teeth 180 samples (M = 80; F = 100 were found to be suitable for measuring secondary dentine following Kedici’s method. Absolute mean error of age was calculated by both methodologies. Results clearly showed that in pooled data, method 1 gave an error of ±10.4 years whereas method 2 exhibited an error of approximately ±13 years. A statistically significant difference was noted in absolute mean error of age between two methods of measuring secondary dentine for age estimation. Further, it was also revealed that teeth extracted for periodontal reasons severely decreased the accuracy of Kedici’s method however, the disease had no effect while estimating age by Gustafson’s method. No significant gender differences were noted in the absolute mean error of age by both methods which suggest that there is no need to separate data on the basis of gender.

  11. A quantitative structure-activity relationship to predict efficacy of granular activated carbon adsorption to control emerging contaminants.

    Science.gov (United States)

    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.

  12. Quantitative structure-activity relationship modelling of oral acute toxicity and cytotoxic activity of fragrance materials in rodents.

    Science.gov (United States)

    Papa, E; Luini, M; Gramatica, P

    2009-10-01

    Fragrance materials are used as ingredients in many consumer and personal care products. The wide and daily use of these substances, as well as their mainly uncontrolled discharge through domestic sewage, make fragrance materials both potential indoor and outdoor air pollutants which are also connected to possible toxic effects on humans (asthma, allergies, headaches). Unfortunately, little is known about the environmental fate and toxicity of these substances. However, the use of alternative, predictive approaches, such as quantitative structure-activity relationships (QSARs), can help in filling the data gap and in the characterization of the environmental and toxicological profile of these substances. In the proposed study, ordinary least squares regression-based QSAR models were developed for three toxicological endpoints: mouse oral LD(50), inhibition of NADH-oxidase (EC(50) NADH-Ox) and the effect on mitochondrial membrane potential (EC(50) DeltaPsim). Theoretical molecular descriptors were calculated by using DRAGON software, and the best QSAR models were developed according to the principles defined by the Organization for Economic Co-operation and Development.

  13. Counseling Persons with Comorbid Disorders: A Quantitative Comparison of Counselor Active Rehabilitation Service and Standard Rehabilitation Counseling Approaches

    Science.gov (United States)

    Ferdinandi, Andrew D.; Li, Ming Hui

    2007-01-01

    The purpose of this quantitative study was to investigate the effect of counselor active rehabilitation service compared with the effect of standard rehabilitation counseling in assisting individuals with coexisting psychiatric and substance abuse disorders in attaining desired life roles. This study was conducted during a 6-month period in a…

  14. Quantitative PET of human urokinase-type plasminogen activator receptor with 64Cu-DOTA-AE105

    DEFF Research Database (Denmark)

    Persson, Morten; Madsen, Jacob; Østergaard, Søren

    2012-01-01

    Expression levels of the urokinase-type plasminogen activator receptor (uPAR) represent an established biomarker for poor prognosis in a variety of human cancers. The objective of the present study was to explore whether noninvasive PET can be used to perform a quantitative assessment of expressi...

  15. A quantitative structure-activity relationship for the acute toxicity of some epoxy compounds to the guppy

    NARCIS (Netherlands)

    Deneer, J.W.; Sinnige, T.L.; Seinen, W.; Hermens, J.L.M.

    1988-01-01

    The 14 day LC50 values of various epoxy compounds to the guppy (Poecilia reticulata) were determined, and investigated through the construction of a quantitative structure-activity relationship (QSAR). Both hydrophobicity and alkylating potency of the compounds are found to be necessary parameters f

  16. Using Gypsum Hydration Water to Quantitatively Estimate the Intensity of the Terminal Classic Drought in the Maya Lowlands

    Science.gov (United States)

    Gázquez, F.; Evans, N. P.; Bauska, T. K.; Hodell, D. A.

    2016-12-01

    Paleoclimate evidence suggests that drought coincided with the collapse of the lowland Classic Maya civilization between 800 and 1000 AD. However, attempts to quantitatively determine the magnitude of hydrologic change have met with mixed results. Several periods of gypsum deposition have been documented in Lake Chichancanab (Yucatan Peninsula, Mexico) sediment cores and interpreted as representing times of drought. Here we analyzed the triple oxygen (17O/16O, 18O/16O) and hydrogen (2H/1H) isotope ratios of the gypsum hydration water to obtain the δ18O, δD, 17O-excess, and d-excess of the lake water during the drought periods. By comparing these results to measurements made on the modern lake, rain and ground waters, we are able to better constrain the hydrological changes that occurred in the lake basin during the Terminal Classic Drought (TCD). During the TCD, the δ18O and δD of the lake water increased compared with modern values, whereas the 17O-excess, and d-excess decreased. The isotopic composition of lake water (δ17O, δ18O and δD, and derived d-excess and 17O-excess) is sensitive to changes in atmospheric relative humidity and temperature. We modeled the isotopic data and found the observed changes can be explained by a 10% reduction in relative humidity compared to modern conditions. This reduction in relative humidity was accompanied by a significant increase in evaporation over precipitation. Furthermore, we show that the driest period occurred during the early phase of the TCD (ca 770-870 AD) when the Classic Maya declined. Previous studies based on stalagmite δ18O records suggested that the greatest drought period occurred in the Postclassic Period (1020 and 1100 AD) and post-dated the collapse. Our findings from Lake Chichancanab suggest that the changes to the hydrological budget during the TCD were greater than those during the early Postclassic Period.

  17. Forensic comparison and matching of fingerprints: using quantitative image measures for estimating error rates through understanding and predicting difficulty.

    Directory of Open Access Journals (Sweden)

    Philip J Kellman

    Full Text Available 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

  18. Forensic comparison and matching of fingerprints: using quantitative image measures for estimating error rates through understanding and predicting difficulty.

    Science.gov (United States)

    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

  19. Estimation of genetic parameters and detection of quantitative trait loci for minerals in Danish Holstein and Danish Jersey milk

    DEFF Research Database (Denmark)

    Buitenhuis, Albert Johannes; Poulsen, Nina Aagaard; Sehested, Jakob

    2015-01-01

    Background Bovine milk provides important minerals, essential for human nutrition and dairy product quality. For changing the mineral composition of the milk to improve dietary needs in human nutrition and technological properties of milk, a thorough understanding of the genetics underlying milk...... mineral contents is important. Therefore the aim of this study was to 1) estimate the genetic parameters for individual minerals in Danish Holstein (DH) (n = 371) and Danish Jersey (DJ) (n = 321) milk, and 2) detect genomic regions associated with mineral content in the milk using a genome...... The results show that Ca, Zn, P and Mg show high heritabilities. In combination with the GWAS results this opens up possibilities to select for specific minerals in bovine milk....

  20. VO2 estimation using 6-axis motion sensor with sports activity classification.

    Science.gov (United States)

    Nagata, Takashi; Nakamura, Naoteru; Miyatake, Masato; Yuuki, Akira; Yomo, Hiroyuki; Kawabata, Takashi; Hara, Shinsuke

    2016-08-01

    In this paper, we focus on oxygen consumption (VO2) estimation using 6-axis motion sensor (3-axis accelerometer and 3-axis gyroscope) for people playing sports with diverse intensities. The VO2 estimated with a small motion sensor can be used to calculate the energy expenditure, however, its accuracy depends on the intensities of various types of activities. In order to achieve high accuracy over a wide range of intensities, we employ an estimation framework that first classifies activities with a simple machine-learning based classification algorithm. We prepare different coefficients of linear regression model for different types of activities, which are determined with training data obtained by experiments. The best-suited model is used for each type of activity when VO2 is estimated. The accuracy of the employed framework depends on the trade-off between the degradation due to classification errors and improvement brought by applying separate, optimum model to VO2 estimation. Taking this trade-off into account, we evaluate the accuracy of the employed estimation framework by using a set of experimental data consisting of VO2 and motion data of people with a wide range of intensities of exercises, which were measured by a VO2 meter and motion sensor, respectively. Our numerical results show that the employed framework can improve the estimation accuracy in comparison to a reference method that uses a common regression model for all types of activities.

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

    Directory of Open Access Journals (Sweden)

    Jing eWang

    2015-05-01

    Full Text Available Flow cytometry (FCM is a commonly used method for estimating genome size in many organisms. The use of flow cytometry 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 minutes at a PI concentration of 100 µg ml-1. The quality of the estimates was not improved by one-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 minutes. 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.

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

    Science.gov (United States)

    Wang, Jing; Liu, Juan; Kang, Ming

    2015-01-01

    Flow cytometry (FCM) is a commonly used method for estimating genome size in many organisms. The use of FCM in plants is influenced by endogenous fluorescence inhibitors and may cause an inaccurate estimation of genome size; thus, falsifying the relationship between genome size and phenotypic traits/ecological performance. Quantitative optimization of FCM methodology minimizes such errors, yet there are few studies detailing this methodology. We selected the genus Primulina, one of the most representative and diverse genera of the Old World Gesneriaceae, to evaluate the methodology effect on determining genome size. Our results showed that buffer choice significantly affected genome size estimation in six out of the eight species examined and altered the 2C-value (DNA content) by as much as 21.4%. The staining duration and propidium iodide (PI) concentration slightly affected the 2C-value. Our experiments showed better histogram quality when the samples were stained for 40 min at a PI concentration of 100 μg ml(-1). The quality of the estimates was not improved by 1-day incubation in the dark at 4°C or by centrifugation. Thus, our study determined an optimum protocol for genome size measurement in Primulina: LB01 buffer supplemented with 100 μg ml(-1) PI and stained for 40 min. This protocol also demonstrated a high universality in other Gesneriaceae genera. We report the genome size of nine Gesneriaceae species for the first time. The results showed substantial genome size variation both within and among the species, with the 2C-value ranging between 1.62 and 2.71 pg. Our study highlights the necessity of optimizing the FCM methodology prior to obtaining reliable genome size estimates in a given taxon.

  3. Augmented multivariate image analysis applied to quantitative structure-activity relationship modeling of the phytotoxicities of benzoxazinone herbicides and related compounds on problematic weeds.

    Science.gov (United States)

    Freitas, Mirlaine R; Matias, Stella V B G; Macedo, Renato L G; Freitas, Matheus P; Venturin, Nelson

    2013-09-11

    Two of major weeds affecting cereal crops worldwide are Avena fatua L. (wild oat) and Lolium rigidum Gaud. (rigid ryegrass). Thus, development of new herbicides against these weeds is required; in line with this, benzoxazinones, their degradation products, and analogues have been shown to be important allelochemicals and natural herbicides. Despite earlier structure-activity studies demonstrating that hydrophobicity (log P) of aminophenoxazines correlates to phytotoxicity, our findings for a series of benzoxazinone derivatives do not show any relationship between phytotoxicity and log P nor with other two usual molecular descriptors. On the other hand, a quantitative structure-activity relationship (QSAR) analysis based on molecular graphs representing structural shape, atomic sizes, and colors to encode other atomic properties performed very accurately for the prediction of phytotoxicities of these compounds against wild oat and rigid ryegrass. Therefore, these QSAR models can be used to estimate the phytotoxicity of new congeners of benzoxazinone herbicides toward A. fatua L. and L. rigidum Gaud.

  4. Using a non-radioisotopic, quantitative TRAP-based me thod detecting telomerase activities in human hepatoma cells

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A non-radioisotopic, quantitative TRAP-based telom erase activity assay was established mainly by using SYBR Green-I staining instead of radioisotope. Comparing with conventional radioisotope based method, it was better in reproducibility and accuracy. Using this method, we found telomerase activities were absent in normal human liver cells, while detected in all of four human hepatoma cell lines (BEL-7404, SMMC-7721, QGY-7903 and HCCM) without significant differences.

  5. Alternative Sensor System and MLP Neural Network for Vehicle Pedal Activity Estimation

    Directory of Open Access Journals (Sweden)

    Ahmed M. Wefky

    2010-04-01

    Full Text Available It is accepted that the activity of the vehicle pedals (i.e., throttle, brake, clutch reflects the driver’s behavior, which is at least partially related to the fuel consumption and vehicle pollutant emissions. This paper presents a solution to estimate the driver activity regardless of the type, model, and year of fabrication of the vehicle. The solution is based on an alternative sensor system (regime engine, vehicle speed, frontal inclination and linear acceleration that reflects the activity of the pedals in an indirect way, to estimate that activity by means of a multilayer perceptron neural network with a single hidden layer.

  6. Quantitative analysis of contrast-enhanced ultrasonography of the bowel wall can predict disease activity in inflammatory bowel disease

    Energy Technology Data Exchange (ETDEWEB)

    Romanini, Laura, E-mail: laura.romanini@libero.it [Department of Radiology, Spedali Civili di Brescia, P.le Spedali Civili, 1, 25123 Brescia (Italy); Passamonti, Matteo, E-mail: matteopassamonti@gmail.com [Department of Radiology-AO Provincia di Lodi, Via Fissiraga, 15, 26900 Lodi (Italy); Navarria, Mario, E-mail: navarria.mario@tiscali.it [Department of Radiology-ASL Vallecamonica-Sebino, Via Manzoni 142, 25040 Esine, BS (Italy); Lanzarotto, Francesco, E-mail: francesco.lanzarotto@spedalicivili.brescia.it [Department of Gastroenterology, Spedali Civili di Brescia, P.le Spedali Civili, 1, 25123 Brescia (Italy); Villanacci, Vincenzo, E-mail: villanac@alice.it [Department of Pathology, Spedali Civili di Brescia, P.le Spedali Civili, 1, 25123 Brescia (Italy); Grazioli, Luigi, E-mail: radiologia1@spedalicivili.brescia.it [Department of Radiology, Spedali Civili di Brescia, P.le Spedali Civili, 1, 25123 Brescia (Italy); Calliada, Fabrizio, E-mail: fabrizio.calliada@gmail.com [Department of Radiology, University of Pavia, Viale Camillo Golgi 19, 27100 Pavia (Italy); Maroldi, Roberto, E-mail: rmaroldi@gmail.com [Department of Radiology, University of Brescia, P.le Spedali Civili, 1, 25123 Brescia (Italy)

    2014-08-15

    Purpose: To evaluate the accuracy of quantitative analysis of bowel wall enhancement in inflammatory bowel disease (IBD) with contrast enhanced ultrasound (CEUS) by comparing the results with vascular density in a biopsy sample from the same area of the intestinal tract, and to determine the usefulness of this analysis for the prediction of disease activity. Materials and methods: This prospective study was approved by our institute's ethics committee and all patients gave written informed consent. We enrolled 33 consecutive adult patients undergoing colonoscopy and biopsy for IBD. All patients underwent CEUS and the results were quantitatively analyzed. Vessel count per high-power field on biopsy specimens was compared with colonoscopy, baseline ultrasonography, and CEUS findings, and with analysis of peak intensity, time to peak, regional blood volume, mean transit time, and regional blood flow. Results in patients with high and low vascular density were compared using Fisher's test, t-test, Pearson's correlation test, and receiver operating characteristic curve (ROC) analysis. Cutoff values were determined using ROC analysis, and sensitivity and specificity were calculated. Results: High vascular density (>265 vessels per field) on histological examination was significantly correlated with active disease on colonoscopy, baseline ultrasonography, and CEUS (p < .0001). Quantitative analysis showed a higher enhancement peak, a shorter time to peak enhancement, a higher regional blood flow and regional blood volume in patients with high vascular density than in those with low vascular density. Cutoff values to distinguish between active and inactive disease were identified for peak enhancement (>40.5%), and regional blood flow (>54.8 ml/min). Conclusion: Quantitative analysis of CEUS data correlates with disease activity as determined by vascular density. Quantitative parameters of CEUS can be used to predict active disease with high sensitivity and

  7. 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

    Science.gov (United States)

    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

  8. Diary days needed to estimate activity among older African-American and Hispanic women.

    Science.gov (United States)

    Eason, Karen E; Masse, Louise C; Kelder, Steven H; Tortolero, Susan R

    2002-08-01

    The purpose of this study was to estimate variation in energy expenditure among older African-American and Hispanic female workers and nonworkers, and identify the number of days of diary self-report necessary to reliably estimate activity. 227 women (111 African-American, 116 Hispanic) from the Women On The Move study completed a 7-d diary and were used in the analysis for this study (mean age 49.3 yr, SD = 7.0; mean weight 77.0 kg, SD = 17.6 kg; mean BMI 30, SD = 6.5). Kcal per day for total activity and specific types of activity were calculated for each subject and used in generalizability analyses. Results indicated that 11 d of activity are needed to reliably estimate total activity for African-American nonworkers and 8 d for Hispanic nonworkers. For workers, 12 d of activity are needed to reliably estimate total activity for African-Americans and 14 d are required for Hispanics. Days of diary self-report required by activity type for African-Americans range from 6 to 48 for nonworkers and from 6 to 30 for workers. For Hispanics, days of diary self-report required by activity type range from 8 to 111 for nonworkers and 7 to 42 for workers. The results of this study indicate the need for more than 7 d of diary self-report to achieve reliable estimates of total activity in older African-American and Hispanic women. The study also found that certain types of activity could be reliably estimated in less than 7 d. However, when there is less variability in the measure/behavior, the reliability is expected to be less and more measurement days are needed to achieve a desired level of reliability.

  9. Quantitative Structure Activity Relationship and Risk Analysis of Some Pesticides in the Goat milk

    Directory of Open Access Journals (Sweden)

    Faqir Muhammad

    2013-01-01

    Full Text Available 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.

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

    Science.gov (United States)

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

    2002-11-07

    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

  11. Quantitative thermography for the estimation of the U-value: state of the art and a case study

    Science.gov (United States)

    Nardi, Iole; Sfarra, Stefano; Ambrosini, Dario

    2014-11-01

    Energy consumption of buildings could be significantly reduced by improving the efficiency of the envelope. Currently, the estimation of the energy performance of existing buildings requires the knowledge of the overall heat transfer coefficient (U-value) of the walls. U-values can be calculated through a theoretical approach, knowing the thermal conductivity and thickness of each material that constitutes the wall stratigraphy, from project data or coring. Alternatively, U-values can be obtained experimentally, through the ISO recommended heat flow meter measurements. Although generally accepted, the heat flow meter method suffers from some disadvantages. Recently, an alternative approach based on infrared thermography (IRT) has been proposed for in situ measurements. Main advantages of this new approach are non invasivity and the possibility of inspecting relatively large areas in real time. In this paper, after a brief description of the state of the art in the field of U-value measurement by IRT, a case study is described. In particular, the results obtained by IRT on an existing building are compared with U-values given by the standard ISO calculation and heat flow meter measurements; advantages and limitations of the new method are outlined. Some suggestions for a successful exploiting of the IRT approach are also given.

  12. Quantitative volcanic susceptibility analysis of Lanzarote and Chinijo Islands based on kernel density estimation via a linear diffusion process

    Science.gov (United States)

    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

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

    Science.gov (United States)

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

    2016-07-01

    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.

  14. Quantitative volcanic susceptibility analysis of Lanzarote and Chinijo Islands based on kernel density estimation via a linear diffusion process

    Science.gov (United States)

    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.

  15. [Quantitative criteria for the estimation of the effectiveness of bioluminescence expression in natural and transgenic luminescent bacteria].

    Science.gov (United States)

    Gusev, A A; Kargatova, T V; Medvedeva, S E; Popova, L Iu

    2008-01-01

    Computation coefficients for estimating the effectiveness of bioluminescence expression in natural luminescent bacteria P. leiognathi 54 and transgenic strain E. coli Z905/pPHL7 bearing lux-operon in multicopy plasmid are suggested, and their use on the molecular, cell, and population levels was considered. It was shown that, on the population level, all transgenic variants got the better of natural variants of P. leiognathi 54 irrespective of the type of lux-operon regulation. On the cell level, in the bright and dim variants of the transgenic strain, the effectiveness of bioluminescence expression increases by several orders. On the level of one lux-operon, the effectiveness of expression of the bright variant of transgenic strain is substantially higher than in the natural bright variant; in dim variants, the efficiency values are similar, and the effectiveness of bioluminescence expression in the dark variant of E. coli Z905-2 /pPHL7 is by two orders lower than that in the dark variant of P. leiognathi 54.

  16. Quantitative volcanic susceptibility analysis of Lanzarote and Chinijo Islands based on kernel density estimation via a linear diffusion process.

    Science.gov (United States)

    Galindo, I; Romero, M C; Sánchez, N; Morales, J M

    2016-06-06

    Risk management stakeholders in high-populated volcanic islands should be provided with the latest high-quality volcanic information. We present here the first volcanic susceptibility map of Lanzarote and Chinijo Islands and their submarine flanks based on updated chronostratigraphical and volcano structural data, as well as on the geomorphological analysis of the bathymetric data of the submarine flanks. The role of the structural elements in the volcanic susceptibility analysis has been reviewed: vents have been considered since they indicate where previous eruptions took place; eruptive fissures provide information about the stress field as they are the superficial expression of the dyke conduit; eroded dykes have been discarded since they are single non-feeder dykes intruded in deep parts of Miocene-Pliocene volcanic edifices; main faults have been taken into account only in those cases where they could modified the superficial movement of magma. The application of kernel density estimation via a linear diffusion process for the volcanic susceptibility assessment has been applied successfully to Lanzarote and could be applied to other fissure volcanic fields worldwide since the results provide information about the probable area where an eruption could take place but also about the main direction of the probable volcanic fissures.

  17. Altered sensorimotor activation patterns in idiopathic dystonia-an activation likelihood estimation meta-analysis of functional brain imaging studies

    DEFF Research Database (Denmark)

    Løkkegaard, Annemette; Herz, Damian M; Haagensen, Brian N;

    2016-01-01

    . Further, study size was usually small including different types of dystonia. Here we performed an activation likelihood estimation (ALE) meta-analysis of functional neuroimaging studies in patients with primary dystonia to test for convergence of dystonia-related alterations in task-related activity....... Hum Brain Mapp 37:547-557, 2016. © 2015 Wiley Periodicals, Inc....

  18. Precipitation evidences on X-Band Synthetic Aperture Radar imagery: an approach for quantitative detection and estimation

    Science.gov (United States)

    Mori, Saverio; Marzano, Frank S.; Montopoli, Mario; Pulvirenti, Luca; Pierdicca, Nazzareno

    2017-04-01

    al. 2014 and Mori et al. 2012); ancillary data, such as local incident angle and land cover, are used. This stage is necessary to tune the precipitation map stage and to avoid severe misinterpretations on the precipitation map routines. The second stage consist of estimating the local cloud attenuation. Finally the precipitation map is estimated, using the the retrieval algorithm developed by Marzano et al. (2011), applied only to pixels where rain is known to be present. Within the FP7 project EartH2Observe we have applied this methodology to 14 study cases, acquired within TSX and CSK missions over Italy and United States. This choice allows analysing both hurricane-like intense events and continental mid-latitude precipitations, with the possibility to verify and validate the proposed methodology through the available weather radar networks. Moreover it allows in same extent analysing the contribution of orography and quality of ancillary data (i.e. landcover). In this work we will discuss the results obtained until now in terms of improved rain cell localization and precipitation quantification.

  19. Structural similarity based kriging for quantitative structure activity and property relationship modeling.

    Science.gov (United States)

    Teixeira, Ana L; Falcao, Andre O

    2014-07-28

    Structurally similar molecules tend to have similar properties, i.e. closer molecules in the molecular space are more likely to yield similar property values while distant molecules are more likely to yield different values. Based on this principle, we propose the use of a new method that takes into account the high dimensionality of the molecular space, predicting chemical, physical, or biological properties based on the most similar compounds with measured properties. This methodology uses ordinary kriging coupled with three different molecular similarity approaches (based on molecular descriptors, fingerprints, and atom matching) which creates an interpolation map over the molecular space that is capable of predicting properties/activities for diverse chemical data sets. The proposed method was tested in two data sets of diverse chemical compounds collected from the literature and preprocessed. One of the data sets contained dihydrofolate reductase inhibition activity data, and the second molecules for which aqueous solubility was known. The overall predictive results using kriging for both data sets comply with the results obtained in the literature using typical QSPR/QSAR approaches. However, the procedure did not involve any type of descriptor selection or even minimal information about each problem, suggesting that this approach is directly applicable to a large spectrum of problems in QSAR/QSPR. Furthermore, the predictive results improve significantly with the similarity threshold between the training and testing compounds, allowing the definition of a confidence threshold of similarity and error estimation for each case inferred. The use of kriging for interpolation over the molecular metric space is independent of the training data set size, and no reparametrizations are necessary when more compounds are added or removed from the set, and increasing the size of the database will consequentially improve the quality of the estimations. Finally it is shown

  20. QUANTITATIVE ESTIMATION OF SOIL EROSION IN THE DRĂGAN RIVER WATERSHED WITH THE U.S.L.E. TYPE ROMSEM MODEL

    Directory of Open Access Journals (Sweden)

    Csaba HORVÁTH

    2008-05-01

    Full Text Available Quantitative estimation of soil erosion in the Drăgan river watershed with the U.S.L.E. type Romsem modelSediment delivered from water erosion causes substantial waterway damages and water quality degradation. A number of factors such as drainage area size, basin slope, climate, land use/land cover may affect sediment delivery processes. The goal of this study is to define a computationally effective suitable soil erosion model in the Drăgan river watershed, for future sedimentation studies. Geographic Information System (GIS is used to determine the Universal Soil Loss Equation Model (U.S.L.E. values of the studied water basin. The methods and approaches used in this study are expected to be applicable in future research and to watersheds in other regions.

  1. Neural networks involved in adolescent reward processing: An activation likelihood estimation meta-analysis of functional neuroimaging studies.

    Science.gov (United States)

    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.

  2. A first calibration of nonmarine ostracod species for the quantitative estimation of Pleistocene climate change in southern Africa

    Science.gov (United States)

    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

  3. Contrast-enhanced 3T MR Perfusion of Musculoskeletal Tumours: T1 Value Heterogeneity Assessment and Evaluation of the Influence of T1 Estimation Methods on Quantitative Parameters.

    Science.gov (United States)

    Gondim Teixeira, Pedro Augusto; Leplat, Christophe; Chen, Bailiang; De Verbizier, Jacques; Beaumont, Marine; Badr, Sammy; Cotten, Anne; Blum, Alain

    2017-06-14

    To evaluate intra-tumour and striated muscle T1 value heterogeneity and the influence of different methods of T1 estimation on the variability of quantitative perfusion parameters. Eighty-two patients with a histologically confirmed musculoskeletal tumour were prospectively included in this study and, with ethics committee approval, underwent contrast-enhanced MR perfusion and T1 mapping. T1 value variations in viable tumour areas and in normal-appearing striated muscle were assessed. In 20 cases, normal muscle perfusion parameters were calculated using three different methods: signal based and gadolinium concentration based on fixed and variable T1 values. Tumour and normal muscle T1 values were significantly different (p = 0.0008). T1 value heterogeneity was higher in tumours than in normal muscle (variation of 19.8% versus 13%). The T1 estimation method had a considerable influence on the variability of perfusion parameters. Fixed T1 values yielded higher coefficients of variation than variable T1 values (mean 109.6 ± 41.8% and 58.3 ± 14.1% respectively). Area under the curve was the least variable parameter (36%). T1 values in musculoskeletal tumours are significantly different and more heterogeneous than normal muscle. Patient-specific T1 estimation is needed for direct inter-patient comparison of perfusion parameters. • T1 value variation in musculoskeletal tumours is considerable. • T1 values in muscle and tumours are significantly different. • Patient-specific T1 estimation is needed for comparison of inter-patient perfusion parameters. • Technical variation is higher in permeability than semiquantitative perfusion parameters.

  4. A fast method for the quantitative estimation of the distribution of hydrophobic and hydrophilic segments in alpha-helices of membrane proteins.

    Science.gov (United States)

    Luzhkov, V B; Surkov, N F

    2000-01-01

    The work presents a fast quantitative approach for estimating the orientations of hydrophilic and hydrophobic regions in the helical wheels of membrane-spanning alpha-helices of transmembrane proteins. The common hydropathy analysis provides an estimate of the integral hydrophobicity in a moving window which scans an amino acid sequence. The new parameter, orientation hydrophobicity, is based on the estimate of hydrophobicity of the angular segment that scans the helical wheel of a given amino acid sequence. The corresponding procedure involves the treatment of transmembrane helices as cylinders with equal surface elements for each amino acid residue. The orientation hydrophobicity, P(phi), phi = 0-360 degrees, of a helical cylinder is given as a sum of hydrophobicities of individual amino acids which are taken as the S-shaped functions of the angle between the centre of amino acid surface element and the centre of the segment. Non-zero contribution to P(phi) comes only from the amino acids belonging to the angular segment for a given angle phi. The size of the angular segment is related to the size of the channel pore. The amplitudes of amino acid S-functions are calibrated in the way that their maximum values (reached when the amino acid is completely exposed into the pore) are equal to the corresponding hydropathy index in the selected scale (here taken as Goldman-Engelman-Steitz hydropathy scale). The given procedure is applied in the studies of three ionic channels with well characterized three-dimensional structures where the channel pore is formed by a bundle of alpha-helices: cholera toxin B, nicotinic acetylcholine homopentameric alpha7 receptor, and phospholamban. The estimated maximum of hydrophilic properties at the helical wheels are in a good agreement with the spatial orientations of alpha-helices in the corresponding channel pores.

  5. Quantitative use of fluorescent in situ hybridization to examine relationships between mycolic acid-containing actinomycetes and foaming in activated sludge plants.

    Science.gov (United States)

    Davenport, R J; Curtis, T P; Goodfellow, M; Stainsby, F M; Bingley, M

    2000-03-01

    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-m(3) 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 x 10(6) cells ml(-1) or 4 x 10(12) 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.

  6. Energy shift estimation of demand response activation on domestic refrigerators – A field test study

    DEFF Research Database (Denmark)

    Lakshmanan, Venkatachalam; Gudmand-Høyer, Kristian; Marinelli, Mattia;

    2014-01-01

    This paper presents a method to estimate the amount of energy that can be shifted during demand response (DR) activation on domestic refrigerator. Though there are many methods for DR activation like load reduction, load shifting and onsite generation, the method under study is load shifting. Ele...

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

    Science.gov (United States)

    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.

  8. Role of Environmental Factors on Resuming Valued Activities Poststroke: A Systematic Review of Qualitative and Quantitative Findings.

    Science.gov (United States)

    Jellema, Sandra; van der Sande, Rob; van Hees, Suzanne; Zajec, Jana; Steultjens, Esther M; Nijhuis-van der Sanden, Maria W

    2016-06-01

    To investigate how reengagement in valued activities poststroke is influenced by environmental factors. PubMed, CINAHL, and PsycINFO were searched to June 2015 using multiple search terms for stroke, activities, disability, and home and community environments, with the following constraints: English, humans, and adults. Studies were included that contained data on how reengagement in valued activities of community-dwelling stroke survivors was influenced by the environment. Two reviewers independently selected the studies. The search yielded 3726 records; 39 studies were eventually included. Findings were extracted from qualitative, quantitative, and mixed-design studies. Two reviewers independently assessed study quality using the Oxford Critical Appraisal Skills Programme lists and independently extracted results. Thematic analysis was conducted on qualitative data, revealing 9 themes related to the iterative nature of the process of reengagement and the associated environmental factors. During the process of reengagement, environmental factors interact with personal and disease-related factors in a gradual process of shaping or abandoning valued activities. The sociocultural context in this case determines what activities are valued and can be resumed by stroke survivors. Social support; activity opportunities and obligations; familiar and accessible environments; resources and reminders; and a step-by-step return facilitate stroke survivors to explore, adapt, resume, and maintain their activities. Social support is helpful at all stages of the process and particularly is important in case stroke survivors are fearful to explore their activity possibilities. The quantitative data identified largely endorsed these findings. No quantitative data were found in respect to the iterative nature of the process, familiar environments, or accessibility. Reengagement in valued activities is a gradual process. In each stage of the process, several environmental factors

  9. Atmospheric Correction of Satellite GF-1/WFV Imagery and Quantitative Estimation of Suspended Particulate Matter in the Yangtze Estuary

    Directory of Open Access Journals (Sweden)

    Pei Shang

    2016-11-01

    Full Text Available The Multispectral Wide Field of View (WFV camera on the Chinese GF-1 satellite, launched in 2013, has advantages of high spatial resolution (16 m, short revisit period (4 days and wide scene swath (800 km compared to the Landsat-8/OLI, which make it an ideal means of monitoring spatial-temporal changes of Suspended Particulate Matter (SPM in large estuaries like the Yangtze Estuary. However, a lack of proper atmospheric correction methods has limited its application in water quality assessment. We propose an atmospheric correction method based on a look up table coupled by the atmosphere radiative transfer model (6S and the water semi-empirical radiative transfer (SERT model for inversion of water-leaving reflectance from GF-1 top-of-atmosphere radiance, and then retrieving SPM concentration from water-leaving radiance reflectance of the Yangtze Estuary and its adjacent sea. Results are validated by the Landsat-8/OLI imagery together with autonomous fixed station data, and influences of human activities (e.g., waterway construction and shipping on SPM distribution are analyzed.

  10. Atmospheric Correction of Satellite GF-1/WFV Imagery and Quantitative Estimation of Suspended Particulate Matter in the Yangtze Estuary.

    Science.gov (United States)

    Shang, Pei; Shen, Fang

    2016-11-25

    The Multispectral Wide Field of View (WFV) camera on the Chinese GF-1 satellite, launched in 2013, has advantages of high spatial resolution (16 m), short revisit period (4 days) and wide scene swath (800 km) compared to the Landsat-8/OLI, which make it an ideal means of monitoring spatial-temporal changes of Suspended Particulate Matter (SPM) in large estuaries like the Yangtze Estuary. However, a lack of proper atmospheric correction methods has limited its application in water quality assessment. We propose an atmospheric correction method based on a look up table coupled by the atmosphere radiative transfer model (6S) and the water semi-empirical radiative transfer (SERT) model for inversion of water-leaving reflectance from GF-1 top-of-atmosphere radiance, and then retrieving SPM concentration from water-leaving radiance reflectance of the Yangtze Estuary and its adjacent sea. Results are validated by the Landsat-8/OLI imagery together with autonomous fixed station data, and influences of human activities (e.g., waterway construction and shipping) on SPM distribution are analyzed.

  11. Quantitative estimation of muscle shear elastic modulus of the upper trapezius with supersonic shear imaging during arm positioning.

    Directory of Open Access Journals (Sweden)

    Hio-Teng Leong

    Full Text Available Pain and tenderness of the upper trapezius are the major complaints among people with chronic neck and shoulder disorders. Hyper-activation and increased muscle tension of the upper trapezius during arm elevation will cause imbalance of the scapular muscle force and contribute to neck and shoulder disorders. Assessing the elasticity of the upper trapezius in different arm positions is therefore important for identifying people at risk so as to give preventive programmes or for monitoring the effectiveness of the intervention programmes for these disorders. This study aimed to establish the reliability of supersonic shear imaging (SSI in quantifying upper trapezius elasticity/shear elastic modulus and its ability to measure the modulation of muscle elasticity during arm elevation. Twenty-eight healthy adults (15 males, 13 females; mean age = 29.6 years were recruited to participate in the study. In each participant, the shear elastic modulus of the upper trapezius while the arm was at rest and at 30° abduction was measured by two operators and twice by operator 1 with a time interval between the measurements. The results showed excellent within- and between-session intra-operator (ICC = 0.87-0.97 and inter-observer (ICC = 0.78-0.83 reliability for the upper trapezius elasticity with the arm at rest and at 30° abduction. An increase of 55.23% of shear elastic modulus from resting to 30° abduction was observed. Our findings demonstrate the possibilities for using SSI to quantify muscle elasticity and its potential role in delineating the modulation of upper trapezius elasticity, which is essential for future studies to compare the differences in shear elastic modulus between normal elasticity and that of individuals with neck and shoulder disorders.

  12. Quantitative structure–activity relationship study of P2X7 receptor inhibitors using combination of principal component analysis and artificial intelligence methods

    Science.gov (United States)

    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

  13. Quantitative structure-activity relationship study of P2X7 receptor inhibitors using combination of principal component analysis and artificial intelligence methods.

    Science.gov (United States)

    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.

  14. Estimates of genetic and environmental contribution to 43 quantitative traits support sharing of a homogeneous environment in an isolated population from South Tyrol, Italy.

    Science.gov (United States)

    Marroni, Fabio; Grazio, Daniela; Pattaro, Cristian; Devoto, Marcella; Pramstaller, Peter

    2008-01-01

    As part of the genomic health care program 'GenNova', we measured 43 quantitative traits in 1,136 subjects living in three isolated villages in South Tyrol (Italy), for which extended genealogical information was available. Thirty-seven of the studied traits had been previously investigated in other populations, while six of them are, to the best of our knowledge, studied here for the first time. For all 43 traits we estimated narrow-sense heritability, individual-specific environmental effects, and shared environmental effects. Estimates of narrow-sense heritability were in good agreement with previous findings. We found significant heritability for all traits; after correcting for multiple testing, all traits except serum concentration of glutamic oxaloacetic transaminase (GOT) and potassium still showed significant heritability. In contrast, the effect of living in the same sibship or village (the so-called sibship and household effects, respectively) was significant for a few traits only, and after correcting for multiple testing no trait showed significant shared environment effect. We suggest that the sharing of a highly similar environment by the subjects included in this study explains the low contribution of the household effects to the overall trait variation. This peculiarity should provide an advantage in gene-mapping projects by reducing environmental bias.

  15. 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

    Science.gov (United States)

    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

  16. Benzimidazole-Based Quinazolines: In Vitro Evaluation, Quantitative Structure-Activity Relationship, and Molecular Modeling as Aurora Kinase Inhibitors.

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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 =…

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

    Science.gov (United States)

    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 =…

  19. Inter- and intra-observer agreement of BI-RADS-based subjective visual estimation of amount of fibroglandular breast tissue with magnetic resonance imaging: comparison to automated quantitative assessment

    Energy Technology Data Exchange (ETDEWEB)

    Wengert, G.J.; Helbich, T.H.; Woitek, R.; Kapetas, P.; Clauser, P.; Baltzer, P.A. [Medical University of Vienna/ Vienna General Hospital, Department of Biomedical Imaging and Image-guided Therapy, Division of Molecular and Gender Imaging, Vienna (Austria); Vogl, W.D. [Medical University of Vienna, Department of Biomedical Imaging and Image-guided Therapy, Computational Imaging Research Lab, Wien (Austria); Weber, M. [Medical University of Vienna, Department of Biomedical Imaging and Image-guided Therapy, Division of General and Pediatric Radiology, Wien (Austria); Meyer-Baese, A. [State University of Florida, Department of Scientific Computing in Medicine, Tallahassee, FL (United States); Pinker, Katja [Medical University of Vienna/ Vienna General Hospital, Department of Biomedical Imaging and Image-guided Therapy, Division of Molecular and Gender Imaging, Vienna (Austria); State University of Florida, Department of Scientific Computing in Medicine, Tallahassee, FL (United States); Memorial Sloan-Kettering Cancer Center, Department of Radiology, Molecular Imaging and Therapy Services, New York City, NY (United States)

    2016-11-15

    To evaluate the inter-/intra-observer agreement of BI-RADS-based subjective visual estimation of the amount of fibroglandular tissue (FGT) with magnetic resonance imaging (MRI), and to investigate whether FGT assessment benefits from an automated, observer-independent, quantitative MRI measurement by comparing both approaches. Eighty women with no imaging abnormalities (BI-RADS 1 and 2) were included in this institutional review board (IRB)-approved prospective study. All women underwent un-enhanced breast MRI. Four radiologists independently assessed FGT with MRI by subjective visual estimation according to BI-RADS. Automated observer-independent quantitative measurement of FGT with MRI was performed using a previously described measurement system. Inter-/intra-observer agreements of qualitative and quantitative FGT measurements were assessed using Cohen's kappa (k). Inexperienced readers achieved moderate inter-/intra-observer agreement and experienced readers a substantial inter- and perfect intra-observer agreement for subjective visual estimation of FGT. Practice and experience reduced observer-dependency. Automated observer-independent quantitative measurement of FGT was successfully performed and revealed only fair to moderate agreement (k = 0.209-0.497) with subjective visual estimations of FGT. Subjective visual estimation of FGT with MRI shows moderate intra-/inter-observer agreement, which can be improved by practice and experience. Automated observer-independent quantitative measurements of FGT are necessary to allow a standardized risk evaluation. (orig.)

  20. Posture and activity recognition and energy expenditure estimation in a wearable platform.

    Science.gov (United States)

    Sazonov, Edward; Hegde, Nagaraj; Browning, Raymond C; Melanson, Edward L; Sazonova, Nadezhda A

    2015-07-01

    The use of wearable sensors coupled with the processing power of mobile phones may be an attractive way to provide real-time feedback about physical activity and energy expenditure (EE). Here, we describe the use of a shoe-based wearable sensor system (SmartShoe) with a mobile phone for real-time recognition of various postures/physical activities and the resulting EE. To deal with processing power and memory limitations of the phone, we compare the use of support vector machines (SVM), multinomial logistic discrimination (MLD), and multilayer perceptrons (MLP) for posture and activity classification followed by activity-branched EE estimation. The algorithms were validated using data from 15 subjects who performed up to 15 different activities of daily living during a 4-h stay in a room calorimeter. MLD and MLP demonstrated activity classification accuracy virtually identical to SVM (∼ 95%) while reducing the running time and the memory requirements by a factor of >10 3. Comparison of per-minute EE estimation using activity-branched models resulted in accurate EE prediction (RMSE = 0.78 kcal/min for SVM and MLD activity classification, 0.77 kcal/min for MLP versus RMSE of 0.75 kcal/min for manual annotation). These results suggest that low-power computational algorithms can be successfully used for real-time physical activity monitoring and EE estimation on a wearable platform.

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

    Science.gov (United States)

    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

  2. Joint torque and angle estimation by using ultrasonic muscle activity sensor

    Science.gov (United States)

    Tsutsui, Yoichiro; Tanaka, Takayuki; Kaneko, Shun'ichi; Feng, Maria Q.

    2005-12-01

    We have proposed a brand-new noninvasive ultrasonic sensor for measuring muscle activities named as Ultrasonic Muscle Activity Sensor (UMS). In the previous paper, the authors achieved to accurately estimate joint torque by using UMS and electromyogram (EMG) which is one of the most popular sensors. This paper aims to realize to measure not only joint torque also joint angle by using UMS and EMG. In order to estimate torque and angle of a knee joint, muscle activities of quadriceps femoris and biceps femoris were measured by both UMS and EMG. These targeted muscles are related to contraction and extension of knee joint. Simultaneously, actual torque on the knee joint caused by these muscles was measured by using torque sensor. The knee joint angle was fixed by torque sensor in the experiment, therefore the measurement was in isometric state. In the result, we found that the estimated torque and angle have high correlation coefficient to actual torque and angle. This means that the sensor can be used for angle estimation as well torque estimation. Therefore, it is shown that the combined use of UMS and EMG is effective to torque and angle estimation.

  3. Arbitrage Activities between Offshore and Domestic Yen Money Markets since the End of the Quantitative Easing Policy

    OpenAIRE

    Teppei Nagano; Eiko Ooka; Naohiko Baba

    2007-01-01

    Transactions in the yen money markets have become active since the end of the quantitative easing policy (QEP) in March 2006. In particular, transactions by foreign financial institutions have been increasing in the offshore markets including the FX swap and euroyen deposit markets, as well as the domestic money markets. This Review surveys the spreads and hence the arbitrage relationship between those offshore markets and the domestic money markets. In the short-term money markets, the sprea...

  4. Quantitative analysis of active pharmaceutical ingredients (APIs) using a potentiometric electronic tongue in a SIA flow system

    OpenAIRE

    2016-01-01

    An advanced potentiometric electronic tongue and Sequential Injection Analysis (SIA) measurement system was applied for the quantitative analysis of mixtures containing three active pharmaceutical ingredients (APIs): acetaminophen, ascorbic acid and acetylsalicylic acid, in the presence of various amounts of caffeine as interferent. The flow-through sensor array was composed of miniaturized classical ion-selective electrodes based on plasticized PVC membranes containing only ion exchangers. P...

  5. Estimating the flash flood quantitative parameters affecting the oil-fields infrastructures in Ras Sudr, Sinai, Egypt, during the January 2010 event

    Directory of Open Access Journals (Sweden)

    Safwat Gabr

    2015-12-01

    Full Text Available This paper aims to quantify the hydrological parameters for the flash flood event of 17th January 2010 in Sinai using multiple sets of remote sensing data and field work for the nongaged catchments (approximately 2100 sq km of the wadis affecting Ras Sudr area, which is heavily occupied by numerous oil fields and related activities. The affected areas were visited, and several cross sections of the main active channels were surveyed to estimate the peak discharge rates. The Tropical Rainfall Monitoring Mission (TRMM data have been used to estimate rainfall parameters for the catchments due to the absence of in situ data. The digital elevation model (DEM of the Shuttle Radar Topography Mission (SRTM was used to extract the hydrographic data following standard procedures and techniques of the Geographic Information Systems (GIS. Both of the surveyed and extracted parameters for the active channels were integrated into GIS to estimate the runoff parameters using the open-channel flow equation of Manning’s. The simulated hydrographs show that the total discharge exceeded 5.7 million cubic meters and the peak discharge rate was 70 cubic meters per second. The mitigation of extreme flash flood is possible by altering the natural flow dispersion over the alluvial fan, and conveying the resulting flows into one adjusted channel.

  6. Three-dimensional ventricular activation imaging by means of equivalent current source modeling and estimation.

    Science.gov (United States)

    Liu, Z; Liu, C; He, B

    2006-01-01

    This paper presents a novel electrocardiographic inverse approach for imaging the 3-D ventricular activation sequence based on the modeling and estimation of the equivalent current density throughout the entire myocardial volume. The spatio-temporal coherence of the ventricular excitation process is utilized to derive the activation time from the estimated time course of the equivalent current density. At each time instant during the period of ventricular activation, the distributed equivalent current density is noninvasively estimated from body surface potential maps (BSPM) using a weighted minimum norm approach with a spatio-temporal regularization strategy based on the singular value decomposition of the BSPMs. The activation time at any given location within the ventricular myocardium is determined as the time point with the maximum local current density estimate. Computer simulation has been performed to evaluate the capability of this approach to image the 3-D ventricular activation sequence initiated from a single pacing site in a physiologically realistic cellular automaton heart model. The simulation results demonstrate that the simulated "true" activation sequence can be accurately reconstructed with an average correlation coefficient of 0.90, relative error of 0.19, and the origin of ventricular excitation can be localized with an average localization error of 5.5 mm for 12 different pacing sites distributed throughout the ventricles.

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

    Science.gov (United States)

    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.

  8. Estimation of dynamic time activity curves from dynamic cardiac SPECT imaging

    Science.gov (United States)

    Hossain, J.; Du, Y.; Links, J.; Rahmim, A.; Karakatsanis, N.; Akhbardeh, A.; Lyons, J.; Frey, E. C.

    2015-04-01

    Whole-heart coronary flow reserve (CFR) may be useful as an early predictor of cardiovascular disease or heart failure. Here we propose a simple method to extract the time-activity curve, an essential component needed for estimating the CFR, for a small number of compartments in the body, such as normal myocardium, blood pool, and ischemic myocardial regions, from SPECT data acquired with conventional cameras using slow rotation. We evaluated the method using a realistic simulation of 99mTc-teboroxime imaging. Uptake of 99mTc-teboroxime based on data from the literature were modeled. Data were simulated using the anatomically-realistic 3D NCAT phantom and an analytic projection code that realistically models attenuation, scatter, and the collimator-detector response. The proposed method was then applied to estimate time activity curves (TACs) for a set of 3D volumes of interest (VOIs) directly from the projections. We evaluated the accuracy and precision of estimated TACs and studied the effects of the presence of perfusion defects that were and were not modeled in the estimation procedure. The method produced good estimates of the myocardial and blood-pool TACS organ VOIs, with average weighted absolute biases of less than 5% for the myocardium and 10% for the blood pool when the true organ boundaries were known and the activity distributions in the organs were uniform. In the presence of unknown perfusion defects, the myocardial TAC was still estimated well (average weighted absolute bias myocardial uptake (product of defect extent and severity) was ≤5%. This indicates that the method was robust to modest model mismatch such as the presence of moderate perfusion defects and uptake nonuniformities. With larger defects where the defect VOI was included in the estimation procedure, the estimated normal myocardial and defect TACs were accurate (average weighted absolute bias ≈5% for a defect with 25% extent and 100% severity).

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

    Science.gov (United States)

    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.

  10. Road Friction Estimation under Complicated Maneuver Conditions for Active Yaw Control

    Institute of Scientific and Technical Information of China (English)

    LI Liang; LI Hongzhi; SONG Jian; YANG Cai; WU Hao

    2009-01-01

    Road friction coefficient is a key factor for the stability control of the vehicle dynamics in the critical conditions. Obviously the vehicle dynamics stability control systems, including the anti-lock brake system(ABS), the traction control system(TCS), and the active yaw control(AYC) system, need the accurate tire and road friction information. However, the simplified method based on the linear tire and vehicle model could not obtain the accurate road friction coefficient for the complicated maneuver of the vehicle. Because the active braking control mode of AYC is different from that of ABS, the road friction coefficient cannot be estimated only with the dynamics states of the tire. With the related dynamics states measured by the sensors of AYC, a comprehensive strategy of the road friction estimation for the active yaw control is brought forward with the sensor fusion technique. Firstly, the variations of the dynamics characteristics of vehicle and tire, and the stability control mode in the steering process are considered, and then the proper road friction estimation methods are brought forward according to the vehicle maneuver process. In the steering maneuver without braking, the comprehensive road friction from the four wheels may be estimated based on the multi-sensor signal fusion method. The estimated values of the road friction reflect the road friction characteristic. When the active brake involved, the road friction coefficient of the braked wheel may be estimated based on the brake pressure and tire forces, the estimated values reflect the road friction between the braked wheel and the road. So the optimal control of the wheel slip rate may be obtained according to the road friction coefficient. The methods proposed in the paper are integrated into the real time controller of AYC, which is matched onto the test vehicle. The ground tests validate the accuracy of the proposed method under the complicated maneuver conditions.

  11. Quantitative Laser Biospeckle Method for the Evaluation of the Activity of Trypanosoma cruzi Using VDRL Plates and Digital Analysis

    Science.gov (United States)

    Grassi, Hilda Cristina; García, Lisbette C.; Lobo-Sulbarán, María Lorena; Velásquez, Ana; Andrades-Grassi, Francisco A.; Cabrera, Humberto; Andrades-Grassi, Jesús E.; Andrades, Efrén D. J.

    2016-01-01

    In this paper we report a quantitative laser Biospeckle method using VDRL plates to monitor the activity of Trypanosoma cruzi and the calibration conditions including three image processing algorithms and three programs (ImageJ and two programs designed in this work). Benznidazole was used as a test drug. Variable volume (constant density) and variable density (constant volume) were used for the quantitative evaluation of parasite activity in calibrated wells of the VDRL plate. The desiccation process within the well was monitored as a function of volume and of the activity of the Biospeckle pattern of the parasites as well as the quantitative effect of the surface parasite quantity (proportion of the object’s plane). A statistical analysis was performed with ANOVA, Tukey post hoc and Descriptive Statistics using R and R Commander. Conditions of volume (100μl) and parasite density (2-4x104 parasites/well, in exponential growth phase), assay time (up to 204min), frame number (11 frames), algorithm and program (RCommander/SAGA) for image processing were selected to test the effect of variable concentrations of benznidazole (0.0195 to 20μg/mL / 0.075 to 76.8μM) at various times (1, 61, 128 and 204min) on the activity of the Biospeckle pattern. The flat wells of the VDRL plate were found to be suitable for the quantitative calibration of the activity of Trypanosoma cruzi using the appropriate algorithm and program. Under these conditions, benznidazole produces at 1min an instantaneous effect on the activity of the Biospeckle pattern of T. cruzi, which remains with a similar profile up to 1 hour. A second effect which is dependent on concentrations above 1.25μg/mL and is statistically different from the effect at lower concentrations causes a decrease in the activity of the Biospeckle pattern. This effect is better detected after 1 hour of drug action. This behavior may be explained by an instantaneous effect on a membrane protein of Trypanosoma cruzi that could

  12. Quantitative Laser Biospeckle Method for the Evaluation of the Activity of Trypanosoma cruzi Using VDRL Plates and Digital Analysis.

    Science.gov (United States)

    Grassi, Hilda Cristina; García, Lisbette C; Lobo-Sulbarán, María Lorena; Velásquez, Ana; Andrades-Grassi, Francisco A; Cabrera, Humberto; Andrades-Grassi, Jesús E; Andrades, Efrén D J

    2016-12-01

    In this paper we report a quantitative laser Biospeckle method using VDRL plates to monitor the activity of Trypanosoma cruzi and the calibration conditions including three image processing algorithms and three programs (ImageJ and two programs designed in this work). Benznidazole was used as a test drug. Variable volume (constant density) and variable density (constant volume) were used for the quantitative evaluation of parasite activity in calibrated wells of the VDRL plate. The desiccation process within the well was monitored as a function of volume and of the activity of the Biospeckle pattern of the parasites as well as the quantitative effect of the surface parasite quantity (proportion of the object's plane). A statistical analysis was performed with ANOVA, Tukey post hoc and Descriptive Statistics using R and R Commander. Conditions of volume (100μl) and parasite density (2-4x104 parasites/well, in exponential growth phase), assay time (up to 204min), frame number (11 frames), algorithm and program (RCommander/SAGA) for image processing were selected to test the effect of variable concentrations of benznidazole (0.0195 to 20μg/mL / 0.075 to 76.8μM) at various times (1, 61, 128 and 204min) on the activity of the Biospeckle pattern. The flat wells of the VDRL plate were found to be suitable for the quantitative calibration of the activity of Trypanosoma cruzi using the appropriate algorithm and program. Under these conditions, benznidazole produces at 1min an instantaneous effect on the activity of the Biospeckle pattern of T. cruzi, which remains with a similar profile up to 1 hour. A second effect which is dependent on concentrations above 1.25μg/mL and is statistically different from the effect at lower concentrations causes a decrease in the activity of the Biospeckle pattern. This effect is better detected after 1 hour of drug action. This behavior may be explained by an instantaneous effect on a membrane protein of Trypanosoma cruzi that could

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

    Science.gov (United States)

    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.

  14. Event-related fMRI studies of false memory: An Activation Likelihood Estimation meta-analysis.

    Science.gov (United States)

    Kurkela, Kyle A; Dennis, Nancy A

    2016-01-29

    Over the last two decades, a wealth of research in the domain of episodic memory has focused on understanding the neural correlates mediating false memories, or memories for events that never happened. While several recent qualitative reviews have attempted to synthesize this literature, methodological differences amongst the empirical studies and a focus on only a sub-set of the findings has limited broader conclusions regarding the neural mechanisms underlying false memories. The current study performed a voxel-wise quantitative meta-analysis using activation likelihood estimation to investigate commonalities within the functional magnetic resonance imaging (fMRI) literature studying false memory. The results were broken down by memory phase (encoding, retrieval), as well as sub-analyses looking at differences in baseline (hit, correct rejection), memoranda (verbal, semantic), and experimental paradigm (e.g., semantic relatedness and perceptual relatedness) within retrieval. Concordance maps identified significant overlap across studies for each analysis. Several regions were identified in the general false retrieval analysis as well as multiple sub-analyses, indicating their ubiquitous, yet critical role in false retrieval (medial superior frontal gyrus, left precentral gyrus, left inferior parietal cortex). Additionally, several regions showed baseline- and paradigm-specific effects (hit/perceptual relatedness: inferior and middle occipital gyrus; CRs: bilateral inferior parietal cortex, precuneus, left caudate). With respect to encoding, analyses showed common activity in the left middle temporal gyrus and anterior cingulate cortex. No analysis identified a common cluster of activation in the medial temporal lobe.

  15. EEG-fMRI Bayesian framework for neural activity estimation: a simulation study

    Science.gov (United States)

    Croce, Pierpaolo; Basti, Alessio; Marzetti, Laura; Zappasodi, Filippo; Del Gratta, Cosimo

    2016-12-01

    Objective. Due to the complementary nature of electroencephalography (EEG) and functional magnetic resonance imaging (fMRI), and given the possibility of simultaneous acquisition, the joint data analysis can afford a better understanding of the underlying neural activity estimation. In this simulation study we want to show the benefit of the joint EEG-fMRI neural activity estimation in a Bayesian framework. Approach. We built a dynamic Bayesian framework in order to perform joint EEG-fMRI neural activity time course estimation. The neural activity is originated by a given brain area and detected by means of both measurement techniques. We have chosen a resting state neural activity situation to address the worst case in terms of the signal-to-noise ratio. To infer information by EEG and fMRI concurrently we used a tool belonging to the sequential Monte Carlo (SMC) methods: the particle filter (PF). Main results. First, despite a high computational cost, we showed the feasibility of such an approach. Second, we obtained an improvement in neural activity reconstruction when using both EEG and fMRI measurements. Significance. The proposed simulation shows the improvements in neural activity reconstruction with EEG-fMRI simultaneous data. The application of such an approach to real data allows a better comprehension of the neural dynamics.

  16. Inter- and intra-observer agreement of BI-RADS-based subjective visual estimation of amount of fibroglandular breast tissue with magnetic resonance imaging: comparison to automated quantitative assessment.

    Science.gov (United States)

    Wengert, G J; Helbich, T H; Woitek, R; Kapetas, P; Clauser, P; Baltzer, P A; Vogl, W-D; Weber, M; Meyer-Baese, A; Pinker, Katja

    2016-11-01

    To evaluate the inter-/intra-observer agreement of BI-RADS-based subjective visual estimation of the amount of fibroglandular tissue (FGT) with magnetic resonance imaging (MRI), and to investigate whether FGT assessment benefits from an automated, observer-independent, quantitative MRI measurement by comparing both approaches. Eighty women with no imaging abnormalities (BI-RADS 1 and 2) were included in this institutional review board (IRB)-approved prospective study. All women underwent un-enhanced breast MRI. Four radiologists independently assessed FGT with MRI by subjective visual estimation according to BI-RADS. Automated observer-independent quantitative measurement of FGT with MRI was performed using a previously described measurement system. Inter-/intra-observer agreements of qualitative and quantitative FGT measurements were assessed using Cohen's kappa (k). Inexperienced readers achieved moderate inter-/intra-observer agreement and experienced readers a substantial inter- and perfect intra-observer agreement for subjective visual estimation of FGT. Practice and experience reduced observer-dependency. Automated observer-independent quantitative measurement of FGT was successfully performed and revealed only fair to moderate agreement (k = 0.209-0.497) with subjective visual estimations of FGT. Subjective visual estimation of FGT with MRI shows moderate intra-/inter-observer agreement, which can be improved by practice and experience. Automated observer-independent quantitative measurements of FGT are necessary to allow a standardized risk evaluation. • Subjective FGT estimation with MRI shows moderate intra-/inter-observer agreement in inexperienced readers. • Inter-observer agreement can be improved by practice and experience. • Automated observer-independent quantitative measurements can provide reliable and standardized assessment of FGT with MRI.

  17. H~ Estimation Approach to Active Noise Control: Theory, Algorithm and Real-Time Implementation

    Directory of Open Access Journals (Sweden)

    Bambang Riyanto

    2003-11-01

    Full Text Available This paper presents an H¥ estimation approach to active control of acoustic noise inside an enclosure. It is shown how H¥ filter theory and algorithm can be effectively applied to active noise control to provide important robustness property. Real-time implementation of the algorithm is performed on Digital Signal Processor. Experimental comparison to conventional FxLMS algorithm for active noise control is presented for both single channel and multichannel cases. While providing some new results, this paper also serves as a brief review on H¥ filter theory and on active noise control.

  18. Quantitative Detection and Biological Propagation of Scrapie Seeding Activity In Vitro Facilitate Use of Prions as Model Pathogens for Disinfection

    Science.gov (United States)

    Pritzkow, Sandra; Wagenführ, Katja; Daus, Martin L.; Boerner, Susann; Lemmer, Karin; Thomzig, Achim; Mielke, Martin; Beekes, Michael

    2011-01-01

    Prions are pathogens with an unusually high tolerance to inactivation and constitute a complex challenge to the re-processing of surgical instruments. On the other hand, however, they provide an informative paradigm which has been exploited successfully for the development of novel broad-range disinfectants simultaneously active also against bacteria, viruses and fungi. Here we report on the development of a methodological platform that further facilitates the use of scrapie prions as model pathogens for disinfection. We used specifically adapted serial protein misfolding cyclic amplification (PMCA) for the quantitative detection, on steel wires providing model carriers for decontamination, of 263K scrapie seeding activity converting normal protease-sensitive into abnormal protease-resistant prion protein. Reference steel wires carrying defined amounts of scrapie infectivity were used for assay calibration, while scrapie-contaminated test steel wires were subjected to fifteen different procedures for disinfection that yielded scrapie titre reductions of ≤101- to ≥105.5-fold. As confirmed by titration in hamsters the residual scrapie infectivity on test wires could be reliably deduced for all examined disinfection procedures, from our quantitative seeding activity assay. Furthermore, we found that scrapie seeding activity present in 263K hamster brain homogenate or multiplied by PMCA of scrapie-contaminated steel wires both triggered accumulation of protease-resistant prion protein and was further propagated in a novel cell assay for 263K scrapie prions, i.e., cerebral glial cell cultures from hamsters. The findings from our PMCA- and glial cell culture assays revealed scrapie seeding activity as a biochemically and biologically replicative principle in vitro, with the former being quantitatively linked to prion infectivity detected on steel wires in vivo. When combined, our in vitro assays provide an alternative to titrations of biological scrapie infectivity

  19. Quantitative detection and biological propagation of scrapie seeding activity in vitro facilitate use of prions as model pathogens for disinfection.

    Directory of Open Access Journals (Sweden)

    Sandra Pritzkow

    Full Text Available Prions are pathogens with an unusually high tolerance to inactivation and constitute a complex challenge to the re-processing of surgical instruments. On the other hand, however, they provide an informative paradigm which has been exploited successfully for the development of novel broad-range disinfectants simultaneously active also against bacteria, viruses and fungi. Here we report on the development of a methodological platform that further facilitates the use of scrapie prions as model pathogens for disinfection. We used specifically adapted serial protein misfolding cyclic amplification (PMCA for the quantitative detection, on steel wires providing model carriers for decontamination, of 263K scrapie seeding activity converting normal protease-sensitive into abnormal protease-resistant prion protein. Reference steel wires carrying defined amounts of scrapie infectivity were used for assay calibration, while scrapie-contaminated test steel wires were subjected to fifteen different procedures for disinfection that yielded scrapie titre reductions of ≤10(1- to ≥10(5.5-fold. As confirmed by titration in hamsters the residual scrapie infectivity on test wires could be reliably deduced for all examined disinfection procedures, from our quantitative seeding activity assay. Furthermore, we found that scrapie seeding activity present in 263K hamster brain homogenate or multiplied by PMCA of scrapie-contaminated steel wires both triggered accumulation of protease-resistant prion protein and was further propagated in a novel cell assay for 263K scrapie prions, i.e., cerebral glial cell cultures from hamsters. The findings from our PMCA- and glial cell culture assays revealed scrapie seeding activity as a biochemically and biologically replicative principle in vitro, with the former being quantitatively linked to prion infectivity detected on steel wires in vivo. When combined, our in vitro assays provide an alternative to titrations of biological

  20. Quantitative detection and biological propagation of scrapie seeding activity in vitro facilitate use of prions as model pathogens for disinfection.

    Science.gov (United States)

    Pritzkow, Sandra; Wagenführ, Katja; Daus, Martin L; Boerner, Susann; Lemmer, Karin; Thomzig, Achim; Mielke, Martin; Beekes, Michael

    2011-01-01

    Prions are pathogens with an unusually high tolerance to inactivation and constitute a complex challenge to the re-processing of surgical instruments. On the other hand, however, they provide an informative paradigm which has been exploited successfully for the development of novel broad-range disinfectants simultaneously active also against bacteria, viruses and fungi. Here we report on the development of a methodological platform that further facilitates the use of scrapie prions as model pathogens for disinfection. We used specifically adapted serial protein misfolding cyclic amplification (PMCA) for the quantitative detection, on steel wires providing model carriers for decontamination, of 263K scrapie seeding activity converting normal protease-sensitive into abnormal protease-resistant prion protein. Reference steel wires carrying defined amounts of scrapie infectivity were used for assay calibration, while scrapie-contaminated test steel wires were subjected to fifteen different procedures for disinfection that yielded scrapie titre reductions of ≤10(1)- to ≥10(5.5)-fold. As confirmed by titration in hamsters the residual scrapie infectivity on test wires could be reliably deduced for all examined disinfection procedures, from our quantitative seeding activity assay. Furthermore, we found that scrapie seeding activity present in 263K hamster brain homogenate or multiplied by PMCA of scrapie-contaminated steel wires both triggered accumulation of protease-resistant prion protein and was further propagated in a novel cell assay for 263K scrapie prions, i.e., cerebral glial cell cultures from hamsters. The findings from our PMCA- and glial cell culture assays revealed scrapie seeding activity as a biochemically and biologically replicative principle in vitro, with the former being quantitatively linked to prion infectivity detected on steel wires in vivo. When combined, our in vitro assays provide an alternative to titrations of biological scrapie

  1. Estimation of the neuronal activation using fMRI data: An observer-based approach

    KAUST Repository

    Laleg-Kirati, Taous-Meriem

    2013-06-01

    This paper deals with the estimation of the neuronal activation and some unmeasured physiological information using the Blood Oxygenation Level Dependent (BOLD) signal measured using functional Magnetic Resonance Imaging (fMRI). We propose to use an observer-based approach applied to the balloon hemodynamic model. The latter describes the relation between the neural activity and the BOLD signal. The balloon model can be expressed in a nonlinear state-space representation where the states, the parameters and the input (neuronal activation), are unknown. This study focuses only on the estimation of the hidden states and the neuronal activation. The model is first linearized around the equilibrium and an observer is applied to this linearized version. Numerical results performed on synthetic data are presented.

  2. Estimating physical activity energy expenditure with the Kinect Sensor in an exergaming environment.

    Directory of Open Access Journals (Sweden)

    David Nathan

    Full Text Available Active video games that require physical exertion during game play have been shown to confer health benefits. Typically, energy expended during game play is measured using devices attached to players, such as accelerometers, or portable gas analyzers. Since 2010, active video gaming technology incorporates marker-less motion capture devices to simulate human movement into game play. Using the Kinect Sensor and Microsoft SDK this research aimed to estimate the mechanical work performed by the human body and estimate subsequent metabolic energy using predictive algorithmic models. Nineteen University students participated in a repeated measures experiment performing four fundamental movements (arm swings, standing jumps, body-weight squats, and jumping jacks. Metabolic energy was captured using a Cortex Metamax 3B automated gas analysis system with mechanical movement captured by the combined motion data from two Kinect cameras. Estimations of the body segment properties, such as segment mass, length, centre of mass position, and radius of gyration, were calculated from the Zatsiorsky-Seluyanov's equations of de Leva, with adjustment made for posture cost. GPML toolbox implementation of the Gaussian Process Regression, a locally weighted k-Nearest Neighbour Regression, and a linear regression technique were evaluated for their performance on predicting the metabolic cost from new feature vectors. The experimental results show that Gaussian Process Regression outperformed the other two techniques by a small margin. This study demonstrated that physical activity energy expenditure during exercise, using the Kinect camera as a motion capture system, can be estimated from segmental mechanical work. Estimates for high-energy activities, such as standing jumps and jumping jacks, can be made accurately, but for low-energy activities, such as squatting, the posture of static poses should be considered as a contributing factor. When translated into the

  3. Levels of plasminogen activator inhibitor type 1 and urokinase plasminogen activator receptor in non-small cell lung cancer as measured by quantitative ELISA and semiquantitative immunohistochemistry

    DEFF Research Database (Denmark)

    Pappot, Helle; Skov, Birgit Guldhammer; Pyke, Charles

    1997-01-01

    The components of the plasminogen activation system have been reported to have prognostic impact in several cancer types, e.g. breast-, colon-, gastric- and lung cancer. Most of these studies have used quantification by enzyme-linked immunosorbent assay (ELISA) on tumour tissue extracts. However...... methodology. In the present study we investigated levels of plasminogen activator inhibitor type 1 (PAI-I) and urokinase plasminogen activator receptor (uPAR), as quantitated by ELISA in tumour extracts from 64 NSCLC patients (38 squamous cell carcinomas, 26 adenocarcinomas), and compared them to staining...

  4. Chromanyl-isoxazolidines as Antibacterial agents: Synthesis, Biological Evaluation, Quantitative Structure Activity Relationship, and Molecular Docking Studies.

    Science.gov (United States)

    Singh, Gagandeep; Sharma, Anuradha; Kaur, Harpreet; Ishar, Mohan Paul S

    2016-02-01

    Regio- and stereoselective 1,3-dipolar cycloadditions of C-(chrom-4-one-3-yl)-N-phenylnitrones (N) with different mono-substituted, disubstituted, and cyclic dipolarophiles were carried out to obtain substituted N-phenyl-3'-(chrom-4-one-3-yl)-isoxazolidines (1-40). All the synthesized compounds were assayed for their in vitro antibacterial activity and display significant inhibitory potential; in particular, compound 32 exhibited good inhibitory activity against Salmonella typhymurium-1 & Salmonella typhymurium-2 with minimum inhibitory concentration value of 1.56 μg/mL and also showed good potential against methicillin-resistant Staphylococcus aureus with minimum inhibitory concentration 3.12 μg/mL. Quantitative structure activity relationship investigations with stepwise multiple linear regression analysis and docking simulation studies have been performed for validation of the observed antibacterial potential of the investigated compounds for determination of the most important parameters regulating antibacterial activities.

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

    Science.gov (United States)

    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.

  6. Improved Age Estimation for Solar-Type Dwarfs Using Activity-Rotation Diagnostics

    CERN Document Server

    Mamajek, Eric E

    2008-01-01

    While the strong anti-correlation between chromospheric activity and age has led to the common use of the Ca II H & K emission index (R'_HK = L_HK/L_bol) as an empirical age estimator for solar type dwarfs, existing activity-age relations produce implausible ages at both high and low activity levels. We have compiled R'_HK data from the literature for young stellar clusters, richly populating for the first time the young end of the activity-age relation. Combining the cluster activity data with modern cluster age estimates, and analyzing the color-dependence of the chromospheric activity age index, we derive an improved activity-age calibration for F7-K2 dwarfs (0.5 < B-V < 0.9 mag). We also present a more fundamentally motivated activity-age calibration that relies on conversion of R'_HK values through the Rossby number to rotation periods, and then makes use of improved gyrochronology relations. We demonstrate that our new activity-age calibration has typical age precision of ~0.2 dex for normal s...

  7. Theoretical and Experimental Investigation of Force Estimation Errors Using Active Magnetic Bearings with Embedded Hall Sensors

    DEFF Research Database (Denmark)

    Voigt, Andreas Jauernik; Santos, Ilmar

    2012-01-01

    This paper gives an original theoretical and experimental contribution to the issue of reducing force estimation errors, which arise when applying Active Magnetic Bearings (AMBs) with pole embedded Hall sensors for force quantification purposes. Motivated by the prospect of increasing the usability...

  8. Assimilation of active and passive microwave observations for improved estimates of soil moisture and crop growth

    Science.gov (United States)

    An Ensemble Kalman Filter-based data assimilation framework that links a crop growth model with active and passive (AP) microwave models was developed to improve estimates of soil moisture (SM) and vegetation biomass over a growing season of soybean. Complementarities in AP observations were incorpo...

  9. The Estimation of Cortical Activity for Brain-Computer Interface: Applications in a Domotic Context

    Directory of Open Access Journals (Sweden)

    F. Babiloni

    2007-01-01

    Full Text Available In order to analyze whether the use of the cortical activity, estimated from noninvasive EEG recordings, could be useful to detect mental states related to the imagination of limb movements, we estimate cortical activity from high-resolution EEG recordings in a group of healthy subjects by using realistic head models. Such cortical activity was estimated in region of interest associated with the subject's Brodmann areas by using a depth-weighted minimum norm technique. Results showed that the use of the cortical-estimated activity instead of the unprocessed EEG improves the recognition of the mental states associated to the limb movement imagination in the group of normal subjects. The BCI methodology presented here has been used in a group of disabled patients in order to give them a suitable control of several electronic devices disposed in a three-room environment devoted to the neurorehabilitation. Four of six patients were able to control several electronic devices in this domotic context with the BCI system.

  10. The estimation of cortical activity for brain-computer interface: applications in a domotic context.

    Science.gov (United States)

    Babiloni, F; Cincotti, F; Marciani, M; Salinari, S; Astolfi, L; Tocci, A; Aloise, F; De Vico Fallani, F; Bufalari, S; Mattia, D

    2007-01-01

    In order to analyze whether the use of the cortical activity, estimated from noninvasive EEG recordings, could be useful to detect mental states related to the imagination of limb movements, we estimate cortical activity from high-resolution EEG recordings in a group of healthy subjects by using realistic head models. Such cortical activity was estimated in region of interest associated with the subject's Brodmann areas by using a depth-weighted minimum norm technique. Results showed that the use of the cortical-estimated activity instead of the unprocessed EEG improves the recognition of the mental states associated to the limb movement imagination in the group of normal subjects. The BCI methodology presented here has been used in a group of disabled patients in order to give them a suitable control of several electronic devices disposed in a three-room environment devoted to the neurorehabilitation. Four of six patients were able to control several electronic devices in this domotic context with the BCI system.

  11. Comparison of Extrapolation and Interpolation Methods for Estimating Daily Photosynthetically Active Radiation (PAR)

    NARCIS (Netherlands)

    Wu, G.; Skidmore, A.K.; Leeuw, de J.; Liu, X.; Prins, H.H.T.

    2010-01-01

    Measurements of photosynthetically active radiation (PAR), which are indispensable for simulating plant growth and productivity, are generally very scarce. This study aimed to compare two extrapolation and one interpolation methods for estimating daily PAR reaching the earth surface within the Poyan

  12. Validity and reliability of Nike + Fuelband for estimating physical activity energy expenditure.

    Science.gov (United States)

    Tucker, Wesley J; Bhammar, Dharini M; Sawyer, Brandon J; Buman, Matthew P; Gaesser, Glenn A

    2015-01-01

    The Nike + Fuelband is a commercially availabl