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Matthew A Sills - One of the best experts on this subject based on the ideXlab platform.
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probing the primary Screening Efficiency by multiple replicate testing a quantitative analysis of hit confirmation and false Screening results of a biochemical assay
Journal of Biomolecular Screening, 2005Co-Authors: Jihu Zhang, Matthew A SillsAbstract:3Despite a large body of references on assay development, assay optimization, strategies, and methodologies for high-throughput Screening (HTS), there have been few reports on investigations of the Efficiency of primary Screening in a systematic and quantitative manner for a typical HTS process. Recently, the authors investigated the primary hit comparison and the effect of measurement variability by Screening a library of approximately 25,000 random compounds in multiple replicate tests in a nuclear receptor recruitment assay with 2 different assay detection technologies. In this report, we utilized these sets of multiple replicate Screening data from a different perspective and conducted a systematic data analysis in order to gain some insights into the hit-finding Efficiency of a typical primary Screening process. Specifically, hit confirmation, false-positive (declaration) rates, and false-negative rates at different hit cutoff limits were explored and calculated from the 2 different assay formats. Results and analyses provided some quantitative estimation regarding the reliability and Efficiency of the primary Screening process. For the 2 assay formats tested in this report, the confirmation rate (activity repeated at or above a certain hit limit) was found to be 65% or above. It was also suggested that, at least in this case, applying some hit-selection strategies, it is possible to decrease the number of false-negative or false-positive hits without significantly increasing the efforts in primary Screening. (Journal of Biomolecular Screening 2005:695-704)
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probing the primary Screening Efficiency by multiple replicate testing a quantitative analysis of hit confirmation and false Screening results of a biochemical assay
Journal of Biomolecular Screening, 2005Co-Authors: Jihu Zhang, Matthew A SillsAbstract:Despite a large body of references on assay development, assay optimization, strategies, and methodologies for high-throughput Screening (HTS), there have been few reports on investigations of the Efficiency of primary Screening in a systematic and quantitative manner for a typical HTS process. Recently, the authors investigated the primary hit comparison and the effect of measurement variability by Screening a library of approximately 25,000 random compounds in multiple replicate tests in a nuclear receptor recruitment assay with 2 different assay detection technologies. In this report, we utilized these sets of multiple replicate Screening data from a different perspective and conducted a systematic data analysis in order to gain some insights into the hit-finding Efficiency of a typical primary Screening process. Specifically, hit confirmation, false-positive (declaration) rates, and false-negative rates at different hit cutoff limits were explored and calculated from the 2 different assay formats. Results and analyses provided some quantitative estimation regarding the reliability and Efficiency of the primary Screening process. For the 2 assay formats tested in this report, the confirmation rate (activity repeated at or above a certain hit limit) was found to be 65% or above. It was also suggested that, at least in this case, applying some hit-selection strategies, it is possible to decrease the number of false-negative or false-positive hits without significantly increasing the efforts in primary Screening.
Howard Cuckle - One of the best experts on this subject based on the ideXlab platform.
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first trimester Screening for down syndrome with ductus venosus doppler studies in addition to nuchal translucency and serum markers
Prenatal Diagnosis, 2005Co-Authors: A Borrell, Anna Gonce, Josep M Martinez, V Borobio, Albert Fortuny, O Coll, Howard CuckleAbstract:Objective To estimate the improvement in Screening Efficiency when fetal ductus venosus Doppler studies are added to existing first-trimester Down syndrome Screening protocols. Methods Statistical modelling was used with parameters derived from prospective ductus venosus studies and from the published literature. The pulsatility index for veins (PIV), was determined in the fetal ductus venosus for 3706 unaffected and 25 Down syndrome pregnancies at 10–14 weeks' gestation. Concurrent nuchal translucency measurement and maternal serum pregnancy associated plasma protein A and free-β human chorionic gonadotrophin were also measured. Results The median PIV in Down syndrome was 1.70 times higher than in unaffected pregnancies (95% confidence interval 1.36–2.12). PIV levels followed an approximately log Gaussian distribution with log10 standard deviations of 0.193 and 0.076 in Down syndrome and unaffected pregnancies. There were no statistically significant correlations between PIV and the other markers. Modelling predicts that for a fixed 5% false-positive rate, the addition of PIV to nuchal translucency alone will increase the detection rate from 76 to 85%, and combined with serum markers, from 88 to 92%. For a fixed 85% detection rate, the false-positive rate reduced from 15 to 4.8% and from 3.2 to 1.2% respectively. Conclusion Ductus venosus Doppler studies can substantially improve Down syndrome Screening Efficiency. Copyright © 2005 John Wiley & Sons, Ltd.
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first trimester Screening for down syndrome in france combining fetal nuchal translucency measurement and biochemical markers
Prenatal Diagnosis, 2003Co-Authors: Françoise Muller, François Audibert, Clarisse Benattar, Sophie Dreux, Nathalie Roussel, Howard CuckleAbstract:Background In France, there is a strictly regulated National Screening Programme for Down syndrome, based on second-trimester maternal serum markers. A prospective study of nuchal translucency together with retrospective evaluation of maternal serum markers was carried out to inform decisions on whether to move the programme to the first trimester. Methods Between January 1998 and June 2001, all women who presented for their prenatal care at 12 participating maternity units were, regardless of age, invited to provide a blood sample and to attend for an NT scan at 11 to 13 weeks. The results were used to derive Gaussian distribution parameters. Detection and false-positive rates were computed in two ways: statistical modelling and directly. The cut-off risk was 1 in 250 at term. Results A total of 5694 women with singleton pregnancies were screened including 26 with Down syndrome and 24 with other aneuploidies. The model-predicted detection and false-positive rates for combined ultrasound and serum Screening were 81 and 4.5% compared to 64 and 6.0% for ultrasound alone. The directly observed rates were 73 and 4.7%, compared to 62 and 5.0% respectively. Conclusion In France, first-trimester Screening with nuchal translucency and maternal serum markers is likely to achieve a high Screening Efficiency. This has important implications for the national Screening policy. Copyright © 2003 John Wiley & Sons, Ltd.
Jihu Zhang - One of the best experts on this subject based on the ideXlab platform.
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probing the primary Screening Efficiency by multiple replicate testing a quantitative analysis of hit confirmation and false Screening results of a biochemical assay
Journal of Biomolecular Screening, 2005Co-Authors: Jihu Zhang, Matthew A SillsAbstract:3Despite a large body of references on assay development, assay optimization, strategies, and methodologies for high-throughput Screening (HTS), there have been few reports on investigations of the Efficiency of primary Screening in a systematic and quantitative manner for a typical HTS process. Recently, the authors investigated the primary hit comparison and the effect of measurement variability by Screening a library of approximately 25,000 random compounds in multiple replicate tests in a nuclear receptor recruitment assay with 2 different assay detection technologies. In this report, we utilized these sets of multiple replicate Screening data from a different perspective and conducted a systematic data analysis in order to gain some insights into the hit-finding Efficiency of a typical primary Screening process. Specifically, hit confirmation, false-positive (declaration) rates, and false-negative rates at different hit cutoff limits were explored and calculated from the 2 different assay formats. Results and analyses provided some quantitative estimation regarding the reliability and Efficiency of the primary Screening process. For the 2 assay formats tested in this report, the confirmation rate (activity repeated at or above a certain hit limit) was found to be 65% or above. It was also suggested that, at least in this case, applying some hit-selection strategies, it is possible to decrease the number of false-negative or false-positive hits without significantly increasing the efforts in primary Screening. (Journal of Biomolecular Screening 2005:695-704)
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probing the primary Screening Efficiency by multiple replicate testing a quantitative analysis of hit confirmation and false Screening results of a biochemical assay
Journal of Biomolecular Screening, 2005Co-Authors: Jihu Zhang, Matthew A SillsAbstract:Despite a large body of references on assay development, assay optimization, strategies, and methodologies for high-throughput Screening (HTS), there have been few reports on investigations of the Efficiency of primary Screening in a systematic and quantitative manner for a typical HTS process. Recently, the authors investigated the primary hit comparison and the effect of measurement variability by Screening a library of approximately 25,000 random compounds in multiple replicate tests in a nuclear receptor recruitment assay with 2 different assay detection technologies. In this report, we utilized these sets of multiple replicate Screening data from a different perspective and conducted a systematic data analysis in order to gain some insights into the hit-finding Efficiency of a typical primary Screening process. Specifically, hit confirmation, false-positive (declaration) rates, and false-negative rates at different hit cutoff limits were explored and calculated from the 2 different assay formats. Results and analyses provided some quantitative estimation regarding the reliability and Efficiency of the primary Screening process. For the 2 assay formats tested in this report, the confirmation rate (activity repeated at or above a certain hit limit) was found to be 65% or above. It was also suggested that, at least in this case, applying some hit-selection strategies, it is possible to decrease the number of false-negative or false-positive hits without significantly increasing the efforts in primary Screening.
Tristan Bereau - One of the best experts on this subject based on the ideXlab platform.
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resolution limit of data driven coarse grained models spanning chemical space
Journal of Chemical Physics, 2019Co-Authors: Kiran H Kanekal, Tristan BereauAbstract:Increasing the Efficiency of materials design remains a significant challenge given the large size of chemical compound space (CCS). The use of a chemically transferable coarse-grained model enables different molecular fragments to map to the same bead type, significantly increasing Screening Efficiency. Here, we propose new criteria for the design of coarse-grained models allowing for the optimization of their chemical transferability and evaluate the Martini model within this framework. We further investigate the scope of this transferability by parameterizing three Martini-like models in which the number of bead types ranges from 5 to 16. These force fields are fully compatible with existing Martini environments because they are parameterized by interpolating the Martini interaction matrix. We then implement a Bayesian approach to determining which chemical groups are likely to be present on fragments corresponding to specific bead types for each model. We demonstrate that a level of accuracy comparable to Martini is obtained with a force field with fewer bead types, using the water/octanol partitioning free energy (ΔGW→Ol) as our metric for comparison. However, the advantage of including more bead types is a reduction of uncertainty when back-mapping these bead types to specific chemistries. Just as reducing the size of the coarse-grained particles leads to a finer mapping of conformational space, increasing the number of bead types yields a finer mapping of CCS. Finally, we note that, due to the large size of fragments mapping to a single Martini bead, a resolution limit arises when using ΔGW→Ol as the only descriptor when coarse-graining CCS.
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resolution limit of data driven coarse grained models spanning chemical space
arXiv: Chemical Physics, 2019Co-Authors: Kiran H Kanekal, Tristan BereauAbstract:Increasing the Efficiency of materials design and discovery remains a significant challenge, especially given the prohibitively large size of chemical compound space. The use of a chemically transferable coarse-grained model enables different molecular fragments to map to the same bead type, while also reducing computational expense. These properties further increase Screening Efficiency, as many compounds are screened through the use of a single coarse-grained simulation, effectively reducing the size of chemical compound space. Here, we propose new criteria for the rational design of coarse-grained models that allows for the optimization of their chemical transferability and evaluate the Martini model within this framework. We further investigate the scope of this chemical transferability by parameterizing three Martini-like models, in which the number of bead types ranges from five to sixteen for the different force fields. We then implement a Bayesian approach to determining which chemical groups are more likely to be present on fragments corresponding to specific bead types for each model. We demonstrate that a level of performance and accuracy comparable to Martini can be obtained by using a force field with fewer bead types. However, the advantage of including more bead types is a reduction of uncertainty with respect to back-mapping these bead types to specific chemistries. Just as reducing the size of the coarse-grained particles leads to a finer mapping of conformational space, increasing the number of bead types yields a finer mapping of chemical compound space. Finally, we note that, due to the relatively large size of the chemical fragments that map to a single martini bead, a clear resolution limit arises when using the water/octanol partition free energy as the only descriptor when coarse-graining chemical compound space.
Yuemin Zhao - One of the best experts on this subject based on the ideXlab platform.
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process analysis and operational parameter optimization of a variable amplitude screen for coal classification
Fuel, 2017Co-Authors: Haishen Jiang, Yuemin Zhao, Chenlong Duan, Jinpeng Qiao, Zengqiang Chen, Enhui Zhou, Hairui Diao, Dahai ZhengAbstract:Abstract Screening is an indispensable unit operation for the large-scale separation of materials. A variable amplitude screen (VAS) has a high Screening Efficiency and reliable performance in coal beneficiation and is widely used for coal classification. In this study, the kinematic characteristics and process analysis of a novel VAS for coal classification were investigated. The vibration test results show that the y axes amplitudes of acceleration and displacement gradually decreased along the material flow. This strengthened the loose and stratification of materials and improved the Screening Efficiency (η) of the VAS. Furthermore, the effects of several operating factors on the Screening performance were studied using Box–Behnken response surface methodology (BBRSM). Based on the experimental data and analysis results, the quadratic model was selected to describe the relationship between η and the operational factors; the sequence of the influencing degree of various factors on η was α > Q > kf > lreb. The optimal operating conditions were obtained by BBRSM analysis and verified by Screening experiments, and the actual Screening Efficiency was 97.18% when the operating conditions were α = 15°, kf = 1.19, lreb = 47.54% and Q = 10.12 t/h, indicating the satisfactory Screening performance of coal in a VAS.
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optimisation of a circularly vibrating screen based on dem simulation and taguchi orthogonal experimental design
Powder Technology, 2017Co-Authors: Yuemin Zhao, Lala Zhao, Chunyong Bao, Qinfu HouAbstract:Abstract In this work, the combined effects of vibration parameters on the circularly Screening processes are analysed based on the Taguchi orthogonal experiment method. First, numerical investigations of the Screening process including the average particle velocity and Screening Efficiency of different particle size fractions are presented. The variations of the average velocity and the Screening Efficiency of different particle size fractions for both spherical and non-spherical particle models are examined. The effect of vibration intensity on the Screening process is discussed and the potential error induced by the analysis of a single factor on the Screening performance is demonstrated. Then, the orthogonal test data of average particle velocity and Screening Efficiency for 16 cases are analysed by using the direct analysis method. The combined effects of amplitude, frequency and the inclination angle of the screen deck on the Screening performance are discussed based on the calculated average values of each level of the factors. The corresponding optimal combinations of the three factors for two Screening performance indexes are obtained, respectively. The effect weights of the vibration parameters on the Screening performance indexes are also obtained by comparing the ranges of the factors. This work should be helpful for the understanding of the combined effects of operation parameters and provides essential references for efficient operation and optimal design of a vibrating screen.
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kinematics of variable amplitude screen and analysis of particle behavior during the process of coal Screening
Powder Technology, 2017Co-Authors: Haishen Jiang, Yuemin Zhao, Chenlong Duan, Jinpeng Qiao, Chusheng Liu, Xuliang Yang, Hairui DiaoAbstract:Abstract Screening is an indispensable unit process for separation of particulate materials in various industrial processes. The variable-amplitude screen (VAS) has been widely used for particle classification because of its large production capacity and good Screening performance. In this paper, a novel VAS driven externally by an unbalanced two-axle excitation was proposed. Kinematics characteristics of the VAS and particle behavior under different operational conditions were investigated using vibration test and dynamic image analysis system. The results show that the displacement amplitude of the VAS decreased gradually along the direction of material flow. Consequently, the migration velocity of particles was larger and the Screening time of particles was long, due to the larger and smaller displacement amplitudes at the feed and discharge ends, respectively. Both of these effects are conducive to improved Screening performance. The operational factors unbalanced excitation force coefficient (kf), relative beam span (lreb) and feed rate (Q) all showed significant influences on the kinematics of the VAS, particle behavior and Screening Efficiency. The difference between the amplitudes of the feed end and the discharge end increased with increasing kf and lreb, thus resulting in the increase of particle velocity; however, these variables showed an inverse relationship with Q. The Screening Efficiency showed a maximum with the increase of all three of the test parameters. It was found that the Screening Efficiency was higher than 94% when kf = 1.22, lreb = 45%, and Q ≤ 4.80 t/h. This indicated that the VAS has excellent performance for coal Screening.
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influence of vibration mode on the Screening process
International journal of mining science and technology, 2013Co-Authors: Hailin Dong, Yuemin Zhao, Chusheng Liu, Lala ZhaoAbstract:Abstract The Screening of particles with different vibration modes was simulated by means of a 3D discrete element method (3D-DEM). The motion and penetration of the particles on the screen deck were analyzed for linear, circular and elliptical vibration of the screen. The results show that the travel velocity of the particles is the fastest, but the Screening Efficiency is the lowest, for the linear vibration mode. The circular motion resulted in the highest Screening Efficiency, but the lowest particle travel velocity. In the steady state the Screening Efficiency for each mode is seen to increase gradually along the longitudinal direction of the deck. The Screening Efficiency increment of the circular mode is the largest while the linear mode shows the smallest increment. The volume fraction of near-mesh size particles at the underside is larger than that of small size particles all along the screen deck. Linear Screening mode has more near-mesh and small size particles on the first three deck sections, and fewer on the last two sections, compared to the circular or elliptical modes.