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Sample records for configuration bias sampling

  1. A new configurational bias scheme for sampling supramolecular structures

    SciTech Connect

    De Gernier, Robin; Mognetti, Bortolo M.; Curk, Tine; Dubacheva, Galina V.; Richter, Ralf P.

    2014-12-28

    We present a new simulation scheme which allows an efficient sampling of reconfigurable supramolecular structures made of polymeric constructs functionalized by reactive binding sites. The algorithm is based on the configurational bias scheme of Siepmann and Frenkel and is powered by the possibility of changing the topology of the supramolecular network by a non-local Monte Carlo algorithm. Such a plan is accomplished by a multi-scale modelling that merges coarse-grained simulations, describing the typical polymer conformations, with experimental results accounting for free energy terms involved in the reactions of the active sites. We test the new algorithm for a system of DNA coated colloids for which we compute the hybridisation free energy cost associated to the binding of tethered single stranded DNAs terminated by short sequences of complementary nucleotides. In order to demonstrate the versatility of our method, we also consider polymers functionalized by receptors that bind a surface decorated by ligands. In particular, we compute the density of states of adsorbed polymers as a function of the number of ligand–receptor complexes formed. Such a quantity can be used to study the conformational properties of adsorbed polymers useful when engineering adsorption with tailored properties. We successfully compare the results with the predictions of a mean field theory. We believe that the proposed method will be a useful tool to investigate supramolecular structures resulting from direct interactions between functionalized polymers for which efficient numerical methodologies of investigation are still lacking.

  2. Interior segment regrowth configurational-bias algorithm for the efficient sampling and fast relaxation of coarse-grained polyethylene and polyoxyethylene melts on a high coordination lattice

    NASA Astrophysics Data System (ADS)

    Rane, Sagar S.; Mattice, Wayne L.

    2005-06-01

    We demonstrate the application of a modified form of the configurational-bias algorithm for the simulation of chain molecules on the second-nearest-neighbor-diamond lattice. Using polyethylene and poly(ethylene-oxide) as model systems we show that the present configurational-bias algorithm can increase the speed of the equilibration by at least a factor of 2-3 or more as compared to the previous method of using a combination of single-bead and pivot moves along with the Metropolis sampling scheme [N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller, J. Chem. Phys. 21, 1087 (1953)]. The increase in the speed of the equilibration is found to be dependent on the interactions (i.e., the polymer being simulated) and the molecular weight of the chains. In addition, other factors not considered, such as the density, would also have a significant effect. The algorithm is an extension of the conventional configurational-bias method adapted to the regrowth of interior segments of chain molecules. Appropriate biasing probabilities for the trial moves as outlined by Jain and de Pablo for the configurational-bias scheme of chain ends, suitably modified for the interior segments, are utilized [T. S. Jain and J. J. de Pablo, in Simulation Methods for Polymers, edited by M. Kotelyanskii and D. N. Theodorou (Marcel Dekker, New York, 2004), pp. 223-255]. The biasing scheme satisfies the condition of detailed balance and produces efficient sampling with the correct equilibrium probability distribution of states. The method of interior regrowth overcomes the limitations of the original configurational-bias scheme and allows for the simulation of polymers of higher molecular weight linear chains and ring polymers which lack chain ends.

  3. Expectancy bias in anxious samples

    PubMed Central

    Cabeleira, Cindy M.; Steinman, Shari A.; Burgess, Melissa M.; Bucks, Romola S.; MacLeod, Colin; Melo, Wilson; Teachman, Bethany A.

    2014-01-01

    While it is well documented that anxious individuals have negative expectations about the future, it is unclear what cognitive processes give rise to this expectancy bias. Two studies are reported that use the Expectancy Task, which is designed to assess expectancy bias and illuminate its basis. This task presents individuals with valenced scenarios (Positive Valence, Negative Valence, or Conflicting Valence), and then evaluates their tendency to expect subsequent future positive relative to negative events. The Expectancy Task was used with low and high trait anxious (Study 1: N = 32) and anxiety sensitive (Study 2: N = 138) individuals. Results suggest that in the context of physical concerns, both high anxious samples display a less positive expectancy bias. In the context of social concerns, high trait anxious individuals display a negative expectancy bias only when negatively valenced information was previously presented. Overall, this suggests that anxious individuals display a less positive expectancy bias, and that the processes that give rise to this bias may vary by type of situation (e.g., social or physical) or anxiety difficulty. PMID:24798678

  4. Heuristic-biased stochastic sampling

    SciTech Connect

    Bresina, J.L.

    1996-12-31

    This paper presents a search technique for scheduling problems, called Heuristic-Biased Stochastic Sampling (HBSS). The underlying assumption behind the HBSS approach is that strictly adhering to a search heuristic often does not yield the best solution and, therefore, exploration off the heuristic path can prove fruitful. Within the HBSS approach, the balance between heuristic adherence and exploration can be controlled according to the confidence one has in the heuristic. By varying this balance, encoded as a bias function, the HBSS approach encompasses a family of search algorithms of which greedy search and completely random search are extreme members. We present empirical results from an application of HBSS to the realworld problem of observation scheduling. These results show that with the proper bias function, it can be easy to outperform greedy search.

  5. Minimising biases in full configuration interaction quantum Monte Carlo.

    PubMed

    Vigor, W A; Spencer, J S; Bearpark, M J; Thom, A J W

    2015-03-14

    We show that Full Configuration Interaction Quantum Monte Carlo (FCIQMC) is a Markov chain in its present form. We construct the Markov matrix of FCIQMC for a two determinant system and hence compute the stationary distribution. These solutions are used to quantify the dependence of the population dynamics on the parameters defining the Markov chain. Despite the simplicity of a system with only two determinants, it still reveals a population control bias inherent to the FCIQMC algorithm. We investigate the effect of simulation parameters on the population control bias for the neon atom and suggest simulation setups to, in general, minimise the bias. We show a reweight ing scheme to remove the bias caused by population control commonly used in diffusion Monte Carlo [Umrigar et al., J. Chem. Phys. 99, 2865 (1993)] is effective and recommend its use as a post processing step.

  6. Role of anisotropy configuration in exchange-biased systems.

    SciTech Connect

    Jimenez, E.; Camarero, J.; Perna, P.; Mikuszeit, N.; Teran, F. J.; Sort, J.; Nogues, J.; Garcia-Martin, J. M.; Hoffmann, A.; Dieny, B.; Miranda, R.

    2011-01-01

    We present a systematic study of the anisotropy configuration effects on the magnetic properties of exchange-biased ferromagnetic/antiferromagnetic (FM/AFM) Co/IrMn bilayers. The interfacial unidirectional anisotropy is set extrinsically via a field cooling procedure with the magnetic field misaligned by an angle {beta}{sub FC} with respect to the intrinsic FM uniaxial anisotropy. High resolution angular dependence in-plane resolved Kerr magnetometry measurements have been performed for three different anisotropy arrangements, including collinear {beta}{sub FC} = 0 and two opposite noncollinear cases. The symmetry breaking of the induced noncollinear configurations results in a peculiar nonsymmetric magnetic behavior of the angular dependence of magnetization reversal, coercivity, and exchange bias. The experimental results are well reproduced without any fitting parameter by using a simple model including the induced anisotropy configuration. Our finding highlights the importance of the relative angle between anisotropies in order to properly account for the magnetic properties of exchange-biased FM/AFM systems.

  7. Sampling Bias on Cup Anemometer Mean Winds

    NASA Astrophysics Data System (ADS)

    Kristensen, L.; Hansen, O. F.; Højstrup, J.

    2003-10-01

    The cup anemometer signal can be sampled in several ways to obtain the mean wind speed. Here we discuss the sampling of series of mean wind speeds from consecutive rotor rotations, followed by unweighted and weighted averaging. It is shown that the unweighted averaging creates a positive bias on the long-term mean wind speed, which is at least one order of magnitude larger than the positive bias from the weighted averaging, also known as the sample-and-hold method. For a homogeneous, neutrally stratified flow the first biases are 1%-2%. For comparison the biases due to fluctuations of the three wind velocity components and due to calibration non-linearity are determined under the same conditions. The largest of these is the v-bias from direction fluctuations. The calculations pertain to the Risø P2546A model cup anemometer.

  8. Semiparametric Regression in Size-Biased Sampling

    PubMed Central

    Chen, Ying Qing

    2009-01-01

    Summary Size-biased sampling arises when a positive-valued outcome variable is sampled with selection probability proportional to its size. In this article, we propose a semiparametric linear regression model to analyze size-biased outcomes. In our proposed model, the regression parameters of the covariates are of major interest, while the distribution of random errors is unspecified. Under the proposed model, we discover that the regression parameters are invariant regardless of size-biased sampling. Following this invariance property, we develop a simple estimation procedure for inferences. Our proposed methods are evaluated in simulation studies and applied to two real data analyses. PMID:19432792

  9. Robust and efficient configurational molecular sampling via Langevin dynamics.

    PubMed

    Leimkuhler, Benedict; Matthews, Charles

    2013-05-07

    A wide variety of numerical methods are evaluated and compared for solving the stochastic differential equations encountered in molecular dynamics. The methods are based on the application of deterministic impulses, drifts, and Brownian motions in some combination. The Baker-Campbell-Hausdorff expansion is used to study sampling accuracy following recent work by the authors, which allows determination of the stepsize-dependent bias in configurational averaging. For harmonic oscillators, configurational averaging is exact for certain schemes, which may result in improved performance in the modelling of biomolecules where bond stretches play a prominent role. For general systems, an optimal method can be identified that has very low bias compared to alternatives. In simulations of the alanine dipeptide reported here (both solvated and unsolvated), higher accuracy is obtained without loss of computational efficiency, while allowing large timestep, and with no impairment of the conformational exploration rate (the effective diffusion rate observed in simulation). The optimal scheme is a uniformly better performing algorithm for molecular sampling, with overall efficiency improvements of 25% or more in practical timestep size achievable in vacuum, and with reductions in the error of configurational averages of a factor of ten or more attainable in solvated simulations at large timestep.

  10. Robust and efficient configurational molecular sampling via Langevin dynamics

    NASA Astrophysics Data System (ADS)

    Leimkuhler, Benedict; Matthews, Charles

    2013-05-01

    A wide variety of numerical methods are evaluated and compared for solving the stochastic differential equations encountered in molecular dynamics. The methods are based on the application of deterministic impulses, drifts, and Brownian motions in some combination. The Baker-Campbell-Hausdorff expansion is used to study sampling accuracy following recent work by the authors, which allows determination of the stepsize-dependent bias in configurational averaging. For harmonic oscillators, configurational averaging is exact for certain schemes, which may result in improved performance in the modelling of biomolecules where bond stretches play a prominent role. For general systems, an optimal method can be identified that has very low bias compared to alternatives. In simulations of the alanine dipeptide reported here (both solvated and unsolvated), higher accuracy is obtained without loss of computational efficiency, while allowing large timestep, and with no impairment of the conformational exploration rate (the effective diffusion rate observed in simulation). The optimal scheme is a uniformly better performing algorithm for molecular sampling, with overall efficiency improvements of 25% or more in practical timestep size achievable in vacuum, and with reductions in the error of configurational averages of a factor of ten or more attainable in solvated simulations at large timestep.

  11. Reduction of switching time in pentalayer nanopillar device with different biasing configurations

    NASA Astrophysics Data System (ADS)

    Aravinthan, D.; Sabareesan, P.; Daniel, M.

    2017-01-01

    The spin transfer torque assisted magnetization switching in a pentalayer nanopillar device is theoretically studied for different biasing configurations. The magnetization switching time is calculated for three different configurations (standard(no biasing), pinned layer biasing and free layer biasing), by numerically solving the governing dynamical Landau-Lifshitz-Gilbert-Slonczewski (LLGS) equation. The corresponding switching time for an applied current density of 3 ×1011Am-2 is about 0.296 ns, 0.195 ns, and 0.108 ns respectively. Pinned layer biasing and free layer biasing increase the magnetization switching speed significantly. Reduction of switching time in the pinned layer biasing is due to the enhancement of spin transfer torque, whereas in the free layer biasing it is due to an additional magnetic torque which arises due to an applied magnetic field. The fastest magnetization switching is achieved for the free layer biasing configuration.

  12. Advanced Biasing Experiments on the C-2 Field-Reversed Configuration Device

    NASA Astrophysics Data System (ADS)

    Thompson, Matthew; Korepanov, Sergey; Garate, Eusebio; Yang, Xiaokang; Gota, Hiroshi; Douglass, Jon; Allfrey, Ian; Valentine, Travis; Uchizono, Nolan; TAE Team

    2014-10-01

    The C-2 experiment seeks to study the evolution, heating and sustainment effects of neutral beam injection on field-reversed configuration (FRC) plasmas. Recently, substantial improvements in plasma performance were achieved through the application of edge biasing with coaxial plasma guns located in the divertors. Edge biasing provides rotation control that reduces instabilities and E × B shear that improves confinement. Typically, the plasma gun arcs are run at ~ 10 MW for the entire shot duration (~ 5 ms), which will become unsustainable as the plasma duration increases. We have conducted several advanced biasing experiments with reduced-average-power plasma gun operating modes and alternative biasing cathodes in an effort to develop an effective biasing scenario applicable to steady state FRC plasmas. Early results show that several techniques can potentially provide effective, long-duration edge biasing.

  13. Selectivity evaluation for two experimental gill-net configurations used to sample Lake Erie walleyes

    USGS Publications Warehouse

    Vandergoot, Christopher S.; Kocovsky, Patrick M.; Brenden, Travis O.; Liu, Weihai

    2011-01-01

    We used length frequencies of captured walleyes Sander vitreus to indirectly estimate and compare selectivity between two experimental gill-net configurations used to sample fish in Lake Erie: (1) a multifilament configuration currently used by the Ohio Department of Natural Resources (ODNR) with stretched-measure mesh sizes ranging from 51 to 127 mm and a constant filament diameter (0.37 mm); and (2) a monofilament configuration with mesh sizes ranging from 38 to 178 mm and varying filament diameter (range = 0.20–0.33 mm). Paired sampling with the two configurations revealed that the catch of walleyes smaller than 250 mm and larger than 600 mm was greater in the monofilament configuration than in the multifilament configuration, but the catch of 250–600-mm fish was greater in the multifilament configuration. Binormal selectivity functions yielded the best fit to observed walleye catches for both gill-net configurations based on model deviances. Incorporation of deviation terms in the binormal selectivity functions (i.e., to relax the assumption of geometric similarity) further improved the fit to observed catches. The final fitted selectivity functions produced results similar to those from the length-based catch comparisons: the monofilament configuration had greater selectivity for small and large walleyes and the multifilament configuration had greater selectivity for mid-sized walleyes. Computer simulations that incorporated the fitted binormal selectivity functions indicated that both nets were likely to result in some bias in age composition estimates and that the degree of bias would ultimately be determined by the underlying condition, mortality rate, and growth rate of the Lake Erie walleye population. Before the ODNR switches its survey gear, additional comparisons of the different gill-net configurations, such as fishing the net pairs across a greater range of depths and at more locations in the lake, should be conducted to maintain congruence in

  14. Effects of spatial configurations on visual change detection: an account of bias changes.

    PubMed

    Boduroglu, Aysecan; Shah, Priti

    2009-12-01

    In order to determine whether people encode spatial configuration information when encoding visual displays, in four experiments, we investigated whether changes in task-irrelevant spatial configuration information would influence color change detection accuracy. In a change detection task, when objects in the test display were presented in new random locations, rather than identical or different locations preserving the overall configuration, participants were more likely to report that the colors had changed. This consistent bias across four experiments suggested that people encode task-irrelevant spatial configuration along with object information. Experiment 4 also demonstrated that only a low-false-alarm group of participants effectively bound spatial configuration information to object information, suggesting that these types of binding processes are open to strategic influences.

  15. Approach-Induced Biases in Human Information Sampling

    PubMed Central

    Hunt, Laurence T.; Rutledge, Robb B.; Malalasekera, W. M. Nishantha; Kennerley, Steven W.; Dolan, Raymond J.

    2016-01-01

    Information sampling is often biased towards seeking evidence that confirms one’s prior beliefs. Despite such biases being a pervasive feature of human behavior, their underlying causes remain unclear. Many accounts of these biases appeal to limitations of human hypothesis testing and cognition, de facto evoking notions of bounded rationality, but neglect more basic aspects of behavioral control. Here, we investigated a potential role for Pavlovian approach in biasing which information humans will choose to sample. We collected a large novel dataset from 32,445 human subjects, making over 3 million decisions, who played a gambling task designed to measure the latent causes and extent of information-sampling biases. We identified three novel approach-related biases, formalized by comparing subject behavior to a dynamic programming model of optimal information gathering. These biases reflected the amount of information sampled (“positive evidence approach”), the selection of which information to sample (“sampling the favorite”), and the interaction between information sampling and subsequent choices (“rejecting unsampled options”). The prevalence of all three biases was related to a Pavlovian approach-avoid parameter quantified within an entirely independent economic decision task. Our large dataset also revealed that individual differences in the amount of information gathered are a stable trait across multiple gameplays and can be related to demographic measures, including age and educational attainment. As well as revealing limitations in cognitive processing, our findings suggest information sampling biases reflect the expression of primitive, yet potentially ecologically adaptive, behavioral repertoires. One such behavior is sampling from options that will eventually be chosen, even when other sources of information are more pertinent for guiding future action. PMID:27832071

  16. Approach-Induced Biases in Human Information Sampling.

    PubMed

    Hunt, Laurence T; Rutledge, Robb B; Malalasekera, W M Nishantha; Kennerley, Steven W; Dolan, Raymond J

    2016-11-01

    Information sampling is often biased towards seeking evidence that confirms one's prior beliefs. Despite such biases being a pervasive feature of human behavior, their underlying causes remain unclear. Many accounts of these biases appeal to limitations of human hypothesis testing and cognition, de facto evoking notions of bounded rationality, but neglect more basic aspects of behavioral control. Here, we investigated a potential role for Pavlovian approach in biasing which information humans will choose to sample. We collected a large novel dataset from 32,445 human subjects, making over 3 million decisions, who played a gambling task designed to measure the latent causes and extent of information-sampling biases. We identified three novel approach-related biases, formalized by comparing subject behavior to a dynamic programming model of optimal information gathering. These biases reflected the amount of information sampled ("positive evidence approach"), the selection of which information to sample ("sampling the favorite"), and the interaction between information sampling and subsequent choices ("rejecting unsampled options"). The prevalence of all three biases was related to a Pavlovian approach-avoid parameter quantified within an entirely independent economic decision task. Our large dataset also revealed that individual differences in the amount of information gathered are a stable trait across multiple gameplays and can be related to demographic measures, including age and educational attainment. As well as revealing limitations in cognitive processing, our findings suggest information sampling biases reflect the expression of primitive, yet potentially ecologically adaptive, behavioral repertoires. One such behavior is sampling from options that will eventually be chosen, even when other sources of information are more pertinent for guiding future action.

  17. Mother-Infant Studies: Subject Refusals and Sampling Bias.

    ERIC Educational Resources Information Center

    Freese, Margaret P.; And Others

    Do sampling biases introduced in studies requiring a large amount of time make those samples less representative than the samples in studies requiring less subject involvement? This question was explored in the context of mother-infant interaction studies by comparing maternal attitudes of two groups of primiparous mothers: 20 mothers who…

  18. Bias Assessment of General Chemistry Analytes using Commutable Samples.

    PubMed

    Koerbin, Gus; Tate, Jillian R; Ryan, Julie; Jones, Graham Rd; Sikaris, Ken A; Kanowski, David; Reed, Maxine; Gill, Janice; Koumantakis, George; Yen, Tina; St John, Andrew; Hickman, Peter E; Simpson, Aaron; Graham, Peter

    2014-11-01

    Harmonisation of reference intervals for routine general chemistry analytes has been a goal for many years. Analytical bias may prevent this harmonisation. To determine if analytical bias is present when comparing methods, the use of commutable samples, or samples that have the same properties as the clinical samples routinely analysed, should be used as reference samples to eliminate the possibility of matrix effect. The use of commutable samples has improved the identification of unacceptable analytical performance in the Netherlands and Spain. The International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) has undertaken a pilot study using commutable samples in an attempt to determine not only country specific reference intervals but to make them comparable between countries. Australia and New Zealand, through the Australasian Association of Clinical Biochemists (AACB), have also undertaken an assessment of analytical bias using commutable samples and determined that of the 27 general chemistry analytes studied, 19 showed sufficiently small between method biases as to not prevent harmonisation of reference intervals. Application of evidence based approaches including the determination of analytical bias using commutable material is necessary when seeking to harmonise reference intervals.

  19. Bias Assessment of General Chemistry Analytes using Commutable Samples

    PubMed Central

    Koerbin, Gus; Tate, Jillian R; Ryan, Julie; Jones, Graham RD; Sikaris, Ken A; Kanowski, David; Reed, Maxine; Gill, Janice; Koumantakis, George; Yen, Tina; St John, Andrew; Hickman, Peter E; Simpson, Aaron; Graham, Peter

    2014-01-01

    Harmonisation of reference intervals for routine general chemistry analytes has been a goal for many years. Analytical bias may prevent this harmonisation. To determine if analytical bias is present when comparing methods, the use of commutable samples, or samples that have the same properties as the clinical samples routinely analysed, should be used as reference samples to eliminate the possibility of matrix effect. The use of commutable samples has improved the identification of unacceptable analytical performance in the Netherlands and Spain. The International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) has undertaken a pilot study using commutable samples in an attempt to determine not only country specific reference intervals but to make them comparable between countries. Australia and New Zealand, through the Australasian Association of Clinical Biochemists (AACB), have also undertaken an assessment of analytical bias using commutable samples and determined that of the 27 general chemistry analytes studied, 19 showed sufficiently small between method biases as to not prevent harmonisation of reference intervals. Application of evidence based approaches including the determination of analytical bias using commutable material is necessary when seeking to harmonise reference intervals. PMID:25678726

  20. Accelerated failure time model under general biased sampling scheme.

    PubMed

    Kim, Jane Paik; Sit, Tony; Ying, Zhiliang

    2016-07-01

    Right-censored time-to-event data are sometimes observed from a (sub)cohort of patients whose survival times can be subject to outcome-dependent sampling schemes. In this paper, we propose a unified estimation method for semiparametric accelerated failure time models under general biased estimating schemes. The proposed estimator of the regression covariates is developed upon a bias-offsetting weighting scheme and is proved to be consistent and asymptotically normally distributed. Large sample properties for the estimator are also derived. Using rank-based monotone estimating functions for the regression parameters, we find that the estimating equations can be easily solved via convex optimization. The methods are confirmed through simulations and illustrated by application to real datasets on various sampling schemes including length-bias sampling, the case-cohort design and its variants. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  1. BIASES IN CASTNET FILTER PACK RESULTS ASSOCIATED WITH SAMPLING PROTOCOL

    EPA Science Inventory

    In the current study, single filter weekly (w) results are compared with weekly results aggregated from day and night (dn) weekly samples. Comparisons of the two sampling protocols for all major constituents (SO42-, NO3-, NH4+, HNO3, and SO2) show median bias (MB) of < 5 nmol m-3...

  2. BIASES IN CASTNET FILTER PACK RESULTS ASSOCIATED WITH SAMPLING PROTOCOL

    EPA Science Inventory

    In the current study, single filter weekly (w) results are compared with weekly results aggregated from day and night (dn) weekly samples. Comparisons of the two sampling protocols for all major constituents (SO42-, NO3-, NH4+, HNO3, and SO2) show median bias (MB) of < 5 nmol m-3...

  3. Ethnic Group's Representation in Test Construction Sample and Test Bias.

    ERIC Educational Resources Information Center

    Fan, Xitao; And Others

    The hypothesis that faulty classical psychometric and sampling procedures in test construction could generate systematic bias against ethnic groups with smaller representation in the test construction sample was studied empirically. Two test construction models were developed: one with differential representation of ethnic groups (White, African…

  4. Sources of Sampling Bias in Long-Screened Well

    EPA Science Inventory

    Results obtained from ground-water sampling in long-screened wells are often influenced by physical factors such as geologic heterogeneity and vertical hydraulic gradients. These factors often serve to bias results and increase uncertainty in the representativeness of the sample...

  5. Network Structure and Biased Variance Estimation in Respondent Driven Sampling

    PubMed Central

    Verdery, Ashton M.; Mouw, Ted; Bauldry, Shawn; Mucha, Peter J.

    2015-01-01

    This paper explores bias in the estimation of sampling variance in Respondent Driven Sampling (RDS). Prior methodological work on RDS has focused on its problematic assumptions and the biases and inefficiencies of its estimators of the population mean. Nonetheless, researchers have given only slight attention to the topic of estimating sampling variance in RDS, despite the importance of variance estimation for the construction of confidence intervals and hypothesis tests. In this paper, we show that the estimators of RDS sampling variance rely on a critical assumption that the network is First Order Markov (FOM) with respect to the dependent variable of interest. We demonstrate, through intuitive examples, mathematical generalizations, and computational experiments that current RDS variance estimators will always underestimate the population sampling variance of RDS in empirical networks that do not conform to the FOM assumption. Analysis of 215 observed university and school networks from Facebook and Add Health indicates that the FOM assumption is violated in every empirical network we analyze, and that these violations lead to substantially biased RDS estimators of sampling variance. We propose and test two alternative variance estimators that show some promise for reducing biases, but which also illustrate the limits of estimating sampling variance with only partial information on the underlying population social network. PMID:26679927

  6. Network Structure and Biased Variance Estimation in Respondent Driven Sampling.

    PubMed

    Verdery, Ashton M; Mouw, Ted; Bauldry, Shawn; Mucha, Peter J

    2015-01-01

    This paper explores bias in the estimation of sampling variance in Respondent Driven Sampling (RDS). Prior methodological work on RDS has focused on its problematic assumptions and the biases and inefficiencies of its estimators of the population mean. Nonetheless, researchers have given only slight attention to the topic of estimating sampling variance in RDS, despite the importance of variance estimation for the construction of confidence intervals and hypothesis tests. In this paper, we show that the estimators of RDS sampling variance rely on a critical assumption that the network is First Order Markov (FOM) with respect to the dependent variable of interest. We demonstrate, through intuitive examples, mathematical generalizations, and computational experiments that current RDS variance estimators will always underestimate the population sampling variance of RDS in empirical networks that do not conform to the FOM assumption. Analysis of 215 observed university and school networks from Facebook and Add Health indicates that the FOM assumption is violated in every empirical network we analyze, and that these violations lead to substantially biased RDS estimators of sampling variance. We propose and test two alternative variance estimators that show some promise for reducing biases, but which also illustrate the limits of estimating sampling variance with only partial information on the underlying population social network.

  7. Field reversed configuration confinement enhancement through edge biasing and neutral beam injection.

    PubMed

    Tuszewski, M; Smirnov, A; Thompson, M C; Korepanov, S; Akhmetov, T; Ivanov, A; Voskoboynikov, R; Schmitz, L; Barnes, D; Binderbauer, M W; Brown, R; Bui, D Q; Clary, R; Conroy, K D; Deng, B H; Dettrick, S A; Douglass, J D; Garate, E; Glass, F J; Gota, H; Guo, H Y; Gupta, D; Gupta, S; Kinley, J S; Knapp, K; Longman, A; Hollins, M; Li, X L; Luo, Y; Mendoza, R; Mok, Y; Necas, A; Primavera, S; Ruskov, E; Schroeder, J H; Sevier, L; Sibley, A; Song, Y; Sun, X; Trask, E; Van Drie, A D; Walters, J K; Wyman, M D

    2012-06-22

    Field reversed configurations (FRCs) with high confinement are obtained in the C-2 device by combining plasma gun edge biasing and neutral beam injection. The plasma gun creates an inward radial electric field that counters the usual FRC spin-up. The n = 2 rotational instability is stabilized without applying quadrupole magnetic fields. The FRCs are nearly axisymmetric, which enables fast ion confinement. The plasma gun also produces E × B shear in the FRC edge layer, which may explain the observed improved particle transport. The FRC confinement times are improved by factors 2 to 4, and the plasma lifetimes are extended from 1 to up to 4 ms.

  8. Effects of Satellite Sampling Configurations on Derived Gridded Fields

    NASA Technical Reports Server (NTRS)

    Lait, Leslie R.

    1998-01-01

    Various configurations of a scanning satellite instrument are simulated by sampling realistic fields of nitrous oxide. Synoptic grids are computed from the resulting simulated orbital data and compared to the original sampled data fields. Results are compared with those obtained by flying a simulated satellite over low-resolution fields and fields that are static in time. Although increasing the number of instrument scan positions does provide more information along an orbital swath, using more than three to five scan positions does not significantly increase the accuracy of global synoptic grids using the gridding techniques described here.

  9. Sample Size Bias in Judgments of Perceptual Averages

    ERIC Educational Resources Information Center

    Price, Paul C.; Kimura, Nicole M.; Smith, Andrew R.; Marshall, Lindsay D.

    2014-01-01

    Previous research has shown that people exhibit a sample size bias when judging the average of a set of stimuli on a single dimension. The more stimuli there are in the set, the greater people judge the average to be. This effect has been demonstrated reliably for judgments of the average likelihood that groups of people will experience negative,…

  10. Imputation for semiparametric transformation models with biased-sampling data

    PubMed Central

    Liu, Hao; Qin, Jing; Shen, Yu

    2012-01-01

    Widely recognized in many fields including economics, engineering, epidemiology, health sciences, technology and wildlife management, length-biased sampling generates biased and right-censored data but often provide the best information available for statistical inference. Different from traditional right-censored data, length-biased data have unique aspects resulting from their sampling procedures. We exploit these unique aspects and propose a general imputation-based estimation method for analyzing length-biased data under a class of flexible semiparametric transformation models. We present new computational algorithms that can jointly estimate the regression coefficients and the baseline function semiparametrically. The imputation-based method under the transformation model provides an unbiased estimator regardless whether the censoring is independent or not on the covariates. We establish large-sample properties using the empirical processes method. Simulation studies show that under small to moderate sample sizes, the proposed procedure has smaller mean square errors than two existing estimation procedures. Finally, we demonstrate the estimation procedure by a real data example. PMID:22903245

  11. Sample Size Bias in Judgments of Perceptual Averages

    ERIC Educational Resources Information Center

    Price, Paul C.; Kimura, Nicole M.; Smith, Andrew R.; Marshall, Lindsay D.

    2014-01-01

    Previous research has shown that people exhibit a sample size bias when judging the average of a set of stimuli on a single dimension. The more stimuli there are in the set, the greater people judge the average to be. This effect has been demonstrated reliably for judgments of the average likelihood that groups of people will experience negative,…

  12. Sample size bias in the estimation of means.

    PubMed

    Smith, Andrew R; Price, Paul C

    2010-08-01

    The present research concerns the hypothesis that intuitive estimates of the arithmetic mean of a sample of numbers tend to increase as a function of the sample size; that is, they reflect a systematic sample size bias. A similar bias has been observed when people judge the average member of a group of people on an inferred quantity (e.g., a disease risk; see Price, 2001; Price, Smith, & Lench, 2006). Until now, however, it has been unclear whether it would be observed when the stimuli were numbers, in which case the quantity need not be inferred, and "average" can be precisely defined as the arithmetic mean. In two experiments, participants estimated the arithmetic mean of 12 samples of numbers. In the first experiment, samples of from 5 to 20 numbers were presented simultaneously and participants quickly estimated their mean. In the second experiment, the numbers in each sample were presented sequentially. The results of both experiments confirmed the existence of a systematic sample size bias.

  13. Sampling Bias in the Molecular Epidemiology of Tuberculosis

    PubMed Central

    2002-01-01

    Among the goals of the molecular epidemiology of infectious disease are to quantify the extent of ongoing transmission of infectious agents and to identify host- and strain-specific risk factors for disease spread. I demonstrate the potential bias in estimates of recent transmission and the impact of risk factors for clustering by using computer simulations to reconstruct populations of tuberculosis patients and sample from them. The bias consistently results in underestimating recent transmission and the impact of risk factors for recent transmission. PMID:11971768

  14. Ensuring Rapid Mixing and Low Bias for Asynchronous Gibbs Sampling

    PubMed Central

    De Sa, Christopher; Olukotun, Kunle; Ré, Christopher

    2016-01-01

    Gibbs sampling is a Markov chain Monte Carlo technique commonly used for estimating marginal distributions. To speed up Gibbs sampling, there has recently been interest in parallelizing it by executing asynchronously. While empirical results suggest that many models can be efficiently sampled asynchronously, traditional Markov chain analysis does not apply to the asynchronous case, and thus asynchronous Gibbs sampling is poorly understood. In this paper, we derive a better understanding of the two main challenges of asynchronous Gibbs: bias and mixing time. We show experimentally that our theoretical results match practical outcomes. PMID:28344730

  15. Nondetection sampling bias in marked presence-only data

    PubMed Central

    Hefley, Trevor J; Tyre, Andrew J; Baasch, David M; Blankenship, Erin E

    2013-01-01

    Species distribution models (SDM) are tools used to determine environmental features that influence the geographic distribution of species' abundance and have been used to analyze presence-only records. Analysis of presence-only records may require correction for nondetection sampling bias to yield reliable conclusions. In addition, individuals of some species of animals may be highly aggregated and standard SDMs ignore environmental features that may influence aggregation behavior. We contend that nondetection sampling bias can be treated as missing data. Statistical theory and corrective methods are well developed for missing data, but have been ignored in the literature on SDMs. We developed a marked inhomogeneous Poisson point process model that accounted for nondetection and aggregation behavior in animals and tested our methods on simulated data. Correcting for nondetection sampling bias requires estimates of the probability of detection which must be obtained from auxiliary data, as presence-only data do not contain information about the detection mechanism. Weighted likelihood methods can be used to correct for nondetection if estimates of the probability of detection are available. We used an inhomogeneous Poisson point process model to model group abundance, a zero-truncated generalized linear model to model group size, and combined these two models to describe the distribution of abundance. Our methods performed well on simulated data when nondetection was accounted for and poorly when detection was ignored. We recommend researchers consider the effects of nondetection sampling bias when modeling species distributions using presence-only data. If information about the detection process is available, we recommend researchers explore the effects of nondetection and, when warranted, correct the bias using our methods. We developed our methods to analyze opportunistic presence-only records of whooping cranes (Grus americana), but expect that our methods will

  16. Nondetection sampling bias in marked presence-only data.

    PubMed

    Hefley, Trevor J; Tyre, Andrew J; Baasch, David M; Blankenship, Erin E

    2013-12-01

    Species distribution models (SDM) are tools used to determine environmental features that influence the geographic distribution of species' abundance and have been used to analyze presence-only records. Analysis of presence-only records may require correction for nondetection sampling bias to yield reliable conclusions. In addition, individuals of some species of animals may be highly aggregated and standard SDMs ignore environmental features that may influence aggregation behavior.We contend that nondetection sampling bias can be treated as missing data. Statistical theory and corrective methods are well developed for missing data, but have been ignored in the literature on SDMs. We developed a marked inhomogeneous Poisson point process model that accounted for nondetection and aggregation behavior in animals and tested our methods on simulated data.Correcting for nondetection sampling bias requires estimates of the probability of detection which must be obtained from auxiliary data, as presence-only data do not contain information about the detection mechanism. Weighted likelihood methods can be used to correct for nondetection if estimates of the probability of detection are available. We used an inhomogeneous Poisson point process model to model group abundance, a zero-truncated generalized linear model to model group size, and combined these two models to describe the distribution of abundance. Our methods performed well on simulated data when nondetection was accounted for and poorly when detection was ignored.We recommend researchers consider the effects of nondetection sampling bias when modeling species distributions using presence-only data. If information about the detection process is available, we recommend researchers explore the effects of nondetection and, when warranted, correct the bias using our methods. We developed our methods to analyze opportunistic presence-only records of whooping cranes (Grus americana), but expect that our methods will be

  17. Estimating Sampling Selection Bias in Human Genetics: A Phenomenological Approach.

    PubMed

    Risso, Davide; Taglioli, Luca; De Iasio, Sergio; Gueresi, Paola; Alfani, Guido; Nelli, Sergio; Rossi, Paolo; Paoli, Giorgio; Tofanelli, Sergio

    2015-01-01

    This research is the first empirical attempt to calculate the various components of the hidden bias associated with the sampling strategies routinely-used in human genetics, with special reference to surname-based strategies. We reconstructed surname distributions of 26 Italian communities with different demographic features across the last six centuries (years 1447-2001). The degree of overlapping between "reference founding core" distributions and the distributions obtained from sampling the present day communities by probabilistic and selective methods was quantified under different conditions and models. When taking into account only one individual per surname (low kinship model), the average discrepancy was 59.5%, with a peak of 84% by random sampling. When multiple individuals per surname were considered (high kinship model), the discrepancy decreased by 8-30% at the cost of a larger variance. Criteria aimed at maximizing locally-spread patrilineages and long-term residency appeared to be affected by recent gene flows much more than expected. Selection of the more frequent family names following low kinship criteria proved to be a suitable approach only for historically stable communities. In any other case true random sampling, despite its high variance, did not return more biased estimates than other selective methods. Our results indicate that the sampling of individuals bearing historically documented surnames (founders' method) should be applied, especially when studying the male-specific genome, to prevent an over-stratification of ancient and recent genetic components that heavily biases inferences and statistics.

  18. Estimating Sampling Selection Bias in Human Genetics: A Phenomenological Approach

    PubMed Central

    Risso, Davide; Taglioli, Luca; De Iasio, Sergio; Gueresi, Paola; Alfani, Guido; Nelli, Sergio; Rossi, Paolo; Paoli, Giorgio; Tofanelli, Sergio

    2015-01-01

    This research is the first empirical attempt to calculate the various components of the hidden bias associated with the sampling strategies routinely-used in human genetics, with special reference to surname-based strategies. We reconstructed surname distributions of 26 Italian communities with different demographic features across the last six centuries (years 1447–2001). The degree of overlapping between "reference founding core" distributions and the distributions obtained from sampling the present day communities by probabilistic and selective methods was quantified under different conditions and models. When taking into account only one individual per surname (low kinship model), the average discrepancy was 59.5%, with a peak of 84% by random sampling. When multiple individuals per surname were considered (high kinship model), the discrepancy decreased by 8–30% at the cost of a larger variance. Criteria aimed at maximizing locally-spread patrilineages and long-term residency appeared to be affected by recent gene flows much more than expected. Selection of the more frequent family names following low kinship criteria proved to be a suitable approach only for historically stable communities. In any other case true random sampling, despite its high variance, did not return more biased estimates than other selective methods. Our results indicate that the sampling of individuals bearing historically documented surnames (founders' method) should be applied, especially when studying the male-specific genome, to prevent an over-stratification of ancient and recent genetic components that heavily biases inferences and statistics. PMID:26452043

  19. Sampling Realistic Protein Conformations Using Local Structural Bias

    PubMed Central

    Hamelryck, Thomas; Kent, John T; Krogh, Anders

    2006-01-01

    The prediction of protein structure from sequence remains a major unsolved problem in biology. The most successful protein structure prediction methods make use of a divide-and-conquer strategy to attack the problem: a conformational sampling method generates plausible candidate structures, which are subsequently accepted or rejected using an energy function. Conceptually, this often corresponds to separating local structural bias from the long-range interactions that stabilize the compact, native state. However, sampling protein conformations that are compatible with the local structural bias encoded in a given protein sequence is a long-standing open problem, especially in continuous space. We describe an elegant and mathematically rigorous method to do this, and show that it readily generates native-like protein conformations simply by enforcing compactness. Our results have far-reaching implications for protein structure prediction, determination, simulation, and design. PMID:17002495

  20. Overcoming Sample Selection Bias in Variable Star Classification

    NASA Astrophysics Data System (ADS)

    Richards, Joseph W.

    With the fast-approaching deluge of photometric data from synoptic surveys, there is an urgent need for methods that quickly and automatically estimate accurate classification probabilities for newly observed sources from a small number of time-series measurements. In Richards et al. [Astrophys J 733:10, 2011, 10.1088/0004-637X/733/1/10], we proposed an end-to-end framework for photometric variable star classification using modern machine learning techniques and demonstrated its accuracy on a single well-studied data set. The methods in that paper assumed that the labeled (training) and unlabeled (testing) sets were drawn from the same underlying population distribution. This is rarely the case in studies of variable stars. Typically, well-understood (labeled) objects form a biased sample of intrinsically brighter, higher signal-to-noise stars. Additionally, data from older surveys are commonly employed to train classifiers that predict the labels of data from active surveys, even though these surveys usually have different characteristics. This problem is referred to in the statistics literature as sample selection bias. Here, I discuss various approaches to this problem and introduce the novel use of cutting-edge machine learning methods, such as co-training and active learning, to overcome sample selection bias in variable star classification. I compare the performance of these methods to standard techniques that ignore the sample selection bias problem. A framework for performing active learning for variable star classification tasks is detailed, and its favorable performance is demonstrated in classifying data from Hipparcos, OGLE, the All Sky Automated Survey, and other modern surveys.

  1. Ensemble-Biased Metadynamics: A Molecular Simulation Method to Sample Experimental Distributions.

    PubMed

    Marinelli, Fabrizio; Faraldo-Gómez, José D

    2015-06-16

    We introduce an enhanced-sampling method for molecular dynamics (MD) simulations referred to as ensemble-biased metadynamics (EBMetaD). The method biases a conventional MD simulation to sample a molecular ensemble that is consistent with one or more probability distributions known a priori, e.g., experimental intramolecular distance distributions obtained by double electron-electron resonance or other spectroscopic techniques. To this end, EBMetaD adds an adaptive biasing potential throughout the simulation that discourages sampling of configurations inconsistent with the target probability distributions. The bias introduced is the minimum necessary to fulfill the target distributions, i.e., EBMetaD satisfies the maximum-entropy principle. Unlike other methods, EBMetaD does not require multiple simulation replicas or the introduction of Lagrange multipliers, and is therefore computationally efficient and straightforward in practice. We demonstrate the performance and accuracy of the method for a model system as well as for spin-labeled T4 lysozyme in explicit water, and show how EBMetaD reproduces three double electron-electron resonance distance distributions concurrently within a few tens of nanoseconds of simulation time. EBMetaD is integrated in the open-source PLUMED plug-in (www.plumed-code.org), and can be therefore readily used with multiple MD engines.

  2. Sampling bias in an internet treatment trial for depression.

    PubMed

    Donkin, L; Hickie, I B; Christensen, H; Naismith, S L; Neal, B; Cockayne, N L; Glozier, N

    2012-10-23

    Internet psychological interventions are efficacious and may reduce traditional access barriers. No studies have evaluated whether any sampling bias exists in these trials that may limit the translation of the results of these trials into real-world application. We identified 7999 potentially eligible trial participants from a community-based health cohort study and invited them to participate in a randomized controlled trial of an online cognitive behavioural therapy programme for people with depression. We compared those who consented to being assessed for trial inclusion with nonconsenters on demographic, clinical and behavioural indicators captured in the health study. Any potentially biasing factors were then assessed for their association with depression outcome among trial participants to evaluate the existence of sampling bias. Of the 35 health survey variables explored, only 4 were independently associated with higher likelihood of consenting-female sex (odds ratio (OR) 1.11, 95% confidence interval (CI) 1.05-1.19), speaking English at home (OR 1.48, 95% CI 1.15-1.90) higher education (OR 1.67, 95% CI 1.46-1.92) and a prior diagnosis of depression (OR 1.37, 95% CI 1.22-1.55). The multivariate model accounted for limited variance (C-statistic 0.6) in explaining participation. These four factors were not significantly associated with either the primary trial outcome measure or any differential impact by intervention arm. This demonstrates that, among eligible trial participants, few factors were associated with the consent to participate. There was no indication that such self-selection biased the trial results or would limit the generalizability and translation into a public or clinical setting.

  3. Sample size bias in retrospective estimates of average duration.

    PubMed

    Smith, Andrew R; Rule, Shanon; Price, Paul C

    2017-03-25

    People often estimate the average duration of several events (e.g., on average, how long does it take to drive from one's home to his or her office). While there is a great deal of research investigating estimates of duration for a single event, few studies have examined estimates when people must average across numerous stimuli or events. The current studies were designed to fill this gap by examining how people's estimates of average duration were influenced by the number of stimuli being averaged (i.e., the sample size). Based on research investigating the sample size bias, we predicted that participants' judgments of average duration would increase as the sample size increased. Across four studies, we demonstrated a sample size bias for estimates of average duration with different judgment types (numeric estimates and comparisons), study designs (between and within-subjects), and paradigms (observing images and performing tasks). The results are consistent with the more general notion that psychological representations of magnitudes in one dimension (e.g., quantity) can influence representations of magnitudes in another dimension (e.g., duration).

  4. Health indicators: eliminating bias from convenience sampling estimators.

    PubMed

    Hedt, Bethany L; Pagano, Marcello

    2011-02-28

    Public health practitioners are often called upon to make inference about a health indicator for a population at large when the sole available information are data gathered from a convenience sample, such as data gathered on visitors to a clinic. These data may be of the highest quality and quite extensive, but the biases inherent in a convenience sample preclude the legitimate use of powerful inferential tools that are usually associated with a random sample. In general, we know nothing about those who do not visit the clinic beyond the fact that they do not visit the clinic. An alternative is to take a random sample of the population. However, we show that this solution would be wasteful if it excluded the use of available information. Hence, we present a simple annealing methodology that combines a relatively small, and presumably far less expensive, random sample with the convenience sample. This allows us to not only take advantage of powerful inferential tools, but also provides more accurate information than that available from just using data from the random sample alone. Copyright © 2011 John Wiley & Sons, Ltd.

  5. Health Indicators: Eliminating bias from convenience sampling estimators

    PubMed Central

    Hedt, Bethany L.; Pagano, Marcello

    2014-01-01

    Public health practitioners are often called upon to make inference about a health indicator for a population at large when the sole available information are data gathered from a convenience sample, such as data gathered on visitors to a clinic. These data may be of the highest quality and quite extensive, but the biases inherent in a convenience sample preclude the legitimate use of powerful inferential tools that are usually associated with a random sample. In general, we know nothing about those who do not visit the clinic beyond the fact that they do not visit the clinic. An alternative is to take a random sample of the population. However, we show that this solution would be wasteful if it excluded the use of available information. So, we present a simple annealing methodology that combines a relatively small, and presumably far less expensive, random sample with the convenience sample. This allows us to not only take advantage of powerful inferential tools, but also provides more accurate information than that available from just using data from the random sample alone. PMID:21290401

  6. Moment and maximum likelihood estimators for Weibull distributions under length- and area-biased sampling

    Treesearch

    Jeffrey H. Gove

    2003-01-01

    Many of the most popular sampling schemes used in forestry are probability proportional to size methods. These methods are also referred to as size biased because sampling is actually from a weighted form of the underlying population distribution. Length- and area-biased sampling are special cases of size-biased sampling where the probability weighting comes from a...

  7. A downhole passive sampling system to avoid bias and error from groundwater sample handling.

    PubMed

    Britt, Sanford L; Parker, Beth L; Cherry, John A

    2010-07-01

    A new downhole groundwater sampler reduces bias and error due to sample handling and exposure while introducing minimal disturbance to natural flow conditions in the formation and well. This "In Situ Sealed", "ISS", or "Snap" sampling device includes removable/lab-ready sample bottles, a sampler device to hold double end-opening sample bottles in an open position, and a line for lowering the sampler system and triggering closure of the bottles downhole. Before deployment, each bottle is set open at both ends to allow flow-through during installation and equilibration downhole. Bottles are triggered to close downhole without well purging; the method is therefore "passive" or "nonpurge". The sample is retrieved in a sealed condition and remains unexposed until analysis. Data from six field studies comparing ISS sampling with traditional methods indicate ISS samples typically yield higher volatile organic compound (VOC) concentrations; in one case, significant chemical-specific differentials between sampling methods were discernible. For arsenic, filtered and unfiltered purge results were negatively and positively biased, respectively, compared to ISS results. Inorganic constituents showed parity with traditional methods. Overall, the ISS is versatile, avoids low VOC recovery bias, and enhances reproducibility while avoiding sampling complexity and purge water disposal.

  8. Reconciling Physical and Seismic Reference Mantle Models: Geographical Sampling Biases

    NASA Astrophysics Data System (ADS)

    Lau, H. C.; Goes, S. D.; Davies, R.

    2012-12-01

    Earth's internal structure is, to a very good first approximation, spherically symmetric. Seismic imaging of lateral anomalies, which are the expression of mantle dynamics, relies on a well-constrained 1-D reference structure. Similarly, interpretation of 3-D seismic structure relies on understanding the physical nature of the 1-D reference. However, plausible physical models of average mantle structure, once converted to seismic velocity, fail to explain the observed 1-D reference velocities. In particular, relative to seismic reference models, the average physical structure for a thermally and chemically well-mixed (i.e., pyrolitic) mantle is: (i) consistently slower in the upper mantle; and (ii) has a higher velocity gradient in the lower mantle. Here, we investigate whether or not geographically biased sampling by the seismic waves used to construct seismic reference models, plays a role in this mismatch. This is done by calculating P-wave travel times through an Earth-like synthetic mantle structure and comparing sampled average synthetic travel times with model average travel times. Our synthetic structure is generated from a global spherical mantle circulation model, in which the geographic distribution of heterogeneity is constrained by 300 million years of plate motion history. Results indicate that geographical biasing is of the same magnitude as the mismatch between our physical model and a seismic reference model. We find that preferential propagation of rays along subduction zones in the upper mantle, together with more uniform sampling by rays in the lower mantle, would lead to a recovered reference model that shows: (i) increased upper mantle velocities; and (ii) a decreased velocity gradient in the lower mantle, when compared to the actual model reference. These tests with P travel times imply that a thermally and chemically well-mixed mantle may actually be consistent with seismic reference mantle models, but further tests with other wave types

  9. Small Sample Sizes Yield Biased Allometric Equations in Temperate Forests

    PubMed Central

    Duncanson, L.; Rourke, O.; Dubayah, R.

    2015-01-01

    Accurate quantification of forest carbon stocks is required for constraining the global carbon cycle and its impacts on climate. The accuracies of forest biomass maps are inherently dependent on the accuracy of the field biomass estimates used to calibrate models, which are generated with allometric equations. Here, we provide a quantitative assessment of the sensitivity of allometric parameters to sample size in temperate forests, focusing on the allometric relationship between tree height and crown radius. We use LiDAR remote sensing to isolate between 10,000 to more than 1,000,000 tree height and crown radius measurements per site in six U.S. forests. We find that fitted allometric parameters are highly sensitive to sample size, producing systematic overestimates of height. We extend our analysis to biomass through the application of empirical relationships from the literature, and show that given the small sample sizes used in common allometric equations for biomass, the average site-level biomass bias is ~+70% with a standard deviation of 71%, ranging from −4% to +193%. These findings underscore the importance of increasing the sample sizes used for allometric equation generation. PMID:26598233

  10. Small Sample Sizes Yield Biased Allometric Equations in Temperate Forests.

    PubMed

    Duncanson, L; Rourke, O; Dubayah, R

    2015-11-24

    Accurate quantification of forest carbon stocks is required for constraining the global carbon cycle and its impacts on climate. The accuracies of forest biomass maps are inherently dependent on the accuracy of the field biomass estimates used to calibrate models, which are generated with allometric equations. Here, we provide a quantitative assessment of the sensitivity of allometric parameters to sample size in temperate forests, focusing on the allometric relationship between tree height and crown radius. We use LiDAR remote sensing to isolate between 10,000 to more than 1,000,000 tree height and crown radius measurements per site in six U.S. forests. We find that fitted allometric parameters are highly sensitive to sample size, producing systematic overestimates of height. We extend our analysis to biomass through the application of empirical relationships from the literature, and show that given the small sample sizes used in common allometric equations for biomass, the average site-level biomass bias is ~+70% with a standard deviation of 71%, ranging from -4% to +193%. These findings underscore the importance of increasing the sample sizes used for allometric equation generation.

  11. Mapping species distributions with MAXENT using a geographically biased sample of presence data: a performance assessment of methods for correcting sampling bias.

    PubMed

    Fourcade, Yoan; Engler, Jan O; Rödder, Dennis; Secondi, Jean

    2014-01-01

    MAXENT is now a common species distribution modeling (SDM) tool used by conservation practitioners for predicting the distribution of a species from a set of records and environmental predictors. However, datasets of species occurrence used to train the model are often biased in the geographical space because of unequal sampling effort across the study area. This bias may be a source of strong inaccuracy in the resulting model and could lead to incorrect predictions. Although a number of sampling bias correction methods have been proposed, there is no consensual guideline to account for it. We compared here the performance of five methods of bias correction on three datasets of species occurrence: one "virtual" derived from a land cover map, and two actual datasets for a turtle (Chrysemys picta) and a salamander (Plethodon cylindraceus). We subjected these datasets to four types of sampling biases corresponding to potential types of empirical biases. We applied five correction methods to the biased samples and compared the outputs of distribution models to unbiased datasets to assess the overall correction performance of each method. The results revealed that the ability of methods to correct the initial sampling bias varied greatly depending on bias type, bias intensity and species. However, the simple systematic sampling of records consistently ranked among the best performing across the range of conditions tested, whereas other methods performed more poorly in most cases. The strong effect of initial conditions on correction performance highlights the need for further research to develop a step-by-step guideline to account for sampling bias. However, this method seems to be the most efficient in correcting sampling bias and should be advised in most cases.

  12. Mapping Species Distributions with MAXENT Using a Geographically Biased Sample of Presence Data: A Performance Assessment of Methods for Correcting Sampling Bias

    PubMed Central

    Fourcade, Yoan; Engler, Jan O.; Rödder, Dennis; Secondi, Jean

    2014-01-01

    MAXENT is now a common species distribution modeling (SDM) tool used by conservation practitioners for predicting the distribution of a species from a set of records and environmental predictors. However, datasets of species occurrence used to train the model are often biased in the geographical space because of unequal sampling effort across the study area. This bias may be a source of strong inaccuracy in the resulting model and could lead to incorrect predictions. Although a number of sampling bias correction methods have been proposed, there is no consensual guideline to account for it. We compared here the performance of five methods of bias correction on three datasets of species occurrence: one “virtual” derived from a land cover map, and two actual datasets for a turtle (Chrysemys picta) and a salamander (Plethodon cylindraceus). We subjected these datasets to four types of sampling biases corresponding to potential types of empirical biases. We applied five correction methods to the biased samples and compared the outputs of distribution models to unbiased datasets to assess the overall correction performance of each method. The results revealed that the ability of methods to correct the initial sampling bias varied greatly depending on bias type, bias intensity and species. However, the simple systematic sampling of records consistently ranked among the best performing across the range of conditions tested, whereas other methods performed more poorly in most cases. The strong effect of initial conditions on correction performance highlights the need for further research to develop a step-by-step guideline to account for sampling bias. However, this method seems to be the most efficient in correcting sampling bias and should be advised in most cases. PMID:24818607

  13. Using Inverse Probability Bootstrap Sampling to Eliminate Sample Induced Bias in Model Based Analysis of Unequal Probability Samples

    PubMed Central

    Nahorniak, Matthew

    2015-01-01

    In ecology, as in other research fields, efficient sampling for population estimation often drives sample designs toward unequal probability sampling, such as in stratified sampling. Design based statistical analysis tools are appropriate for seamless integration of sample design into the statistical analysis. However, it is also common and necessary, after a sampling design has been implemented, to use datasets to address questions that, in many cases, were not considered during the sampling design phase. Questions may arise requiring the use of model based statistical tools such as multiple regression, quantile regression, or regression tree analysis. However, such model based tools may require, for ensuring unbiased estimation, data from simple random samples, which can be problematic when analyzing data from unequal probability designs. Despite numerous method specific tools available to properly account for sampling design, too often in the analysis of ecological data, sample design is ignored and consequences are not properly considered. We demonstrate here that violation of this assumption can lead to biased parameter estimates in ecological research. In addition, to the set of tools available for researchers to properly account for sampling design in model based analysis, we introduce inverse probability bootstrapping (IPB). Inverse probability bootstrapping is an easily implemented method for obtaining equal probability re-samples from a probability sample, from which unbiased model based estimates can be made. We demonstrate the potential for bias in model-based analyses that ignore sample inclusion probabilities, and the effectiveness of IPB sampling in eliminating this bias, using both simulated and actual ecological data. For illustration, we considered three model based analysis tools—linear regression, quantile regression, and boosted regression tree analysis. In all models, using both simulated and actual ecological data, we found inferences to be

  14. Using Inverse Probability Bootstrap Sampling to Eliminate Sample Induced Bias in Model Based Analysis of Unequal Probability Samples.

    PubMed

    Nahorniak, Matthew; Larsen, David P; Volk, Carol; Jordan, Chris E

    2015-01-01

    In ecology, as in other research fields, efficient sampling for population estimation often drives sample designs toward unequal probability sampling, such as in stratified sampling. Design based statistical analysis tools are appropriate for seamless integration of sample design into the statistical analysis. However, it is also common and necessary, after a sampling design has been implemented, to use datasets to address questions that, in many cases, were not considered during the sampling design phase. Questions may arise requiring the use of model based statistical tools such as multiple regression, quantile regression, or regression tree analysis. However, such model based tools may require, for ensuring unbiased estimation, data from simple random samples, which can be problematic when analyzing data from unequal probability designs. Despite numerous method specific tools available to properly account for sampling design, too often in the analysis of ecological data, sample design is ignored and consequences are not properly considered. We demonstrate here that violation of this assumption can lead to biased parameter estimates in ecological research. In addition, to the set of tools available for researchers to properly account for sampling design in model based analysis, we introduce inverse probability bootstrapping (IPB). Inverse probability bootstrapping is an easily implemented method for obtaining equal probability re-samples from a probability sample, from which unbiased model based estimates can be made. We demonstrate the potential for bias in model-based analyses that ignore sample inclusion probabilities, and the effectiveness of IPB sampling in eliminating this bias, using both simulated and actual ecological data. For illustration, we considered three model based analysis tools--linear regression, quantile regression, and boosted regression tree analysis. In all models, using both simulated and actual ecological data, we found inferences to be

  15. Collecting a better water-quality sample: Reducing vertical stratification bias in open and closed channels

    USGS Publications Warehouse

    Selbig, William R.

    2017-01-01

    Collection of water-quality samples that accurately characterize average particle concentrations and distributions in channels can be complicated by large sources of variability. The U.S. Geological Survey (USGS) developed a fully automated Depth-Integrated Sample Arm (DISA) as a way to reduce bias and improve accuracy in water-quality concentration data. The DISA was designed to integrate with existing autosampler configurations commonly used for the collection of water-quality samples in vertical profile thereby providing a better representation of average suspended sediment and sediment-associated pollutant concentrations and distributions than traditional fixed-point samplers. In controlled laboratory experiments, known concentrations of suspended sediment ranging from 596 to 1,189 mg/L were injected into a 3 foot diameter closed channel (circular pipe) with regulated flows ranging from 1.4 to 27.8 ft3 /s. Median suspended sediment concentrations in water-quality samples collected using the DISA were within 7 percent of the known, injected value compared to 96 percent for traditional fixed-point samplers. Field evaluation of this technology in open channel fluvial systems showed median differences between paired DISA and fixed-point samples to be within 3 percent. The range of particle size measured in the open channel was generally that of clay and silt. Differences between the concentration and distribution measured between the two sampler configurations could potentially be much larger in open channels that transport larger particles, such as sand.

  16. Low sampling rates bias outcomes from the Wingate test.

    PubMed

    Santos, E L; Novaes, J S; Reis, V M; Giannella-Neto, A

    2010-11-01

    The purpose of this work was to apply a simple method for acquisition of power output (PO) during the Wingate Anaerobic Test (WAnT) at a high sampling rate ( S(R)) and to compare the effect of lower S(R) on the measurements extracted from the PO. 26 male subjects underwent 2 WAnTs on a cycle ergometer. The reference PO was calculated at 30 Hz as a function of the linear velocity, the moment of inertia and the frictional load. The PO was sampled at 0.2, 0.5, 1, 2 and 5 Hz. Both the peak (16.03±2.22 W·kg (-1)) and mean PO (10.34±1.01 W·kg (-1)) presented lower relative values when the S(R) was lower. Peak PO was attenuated by 0.29-42.07% for decreasing sampling rates, resulting in different values for 0.2 and 1 Hz ( P<0.001). When the S(R) was 0.2 Hz, the time to peak was delayed by 53.81% ( P<0.001) and the fatigue index was attenuated by 22.12% ( P<0.001). In conclusion, due to the differences achieved here and the fact that the peak flywheel frequency is around 2.3 Hz, we strongly recommend that the PO be sampled at 5 Hz instead of 0.2 Hz in order to avoid biased errors and misunderstandings of the WAnT results.

  17. [Several common biases and control measures during sampling survey of eye diseases in China].

    PubMed

    Guan, Huai-jin

    2008-06-01

    Bias is a common artificial error during sampling survey in eye diseases, and is a major impact factor for validity and reliability of the survey. The causes and the control measures of several biases regarding current sampling survey of eye diseases in China were analyzed and discussed, including the sampling bias, non-respondent bias, and diagnostic bias. This review emphasizes that controlling bias is the key to ensure quality of sampling survey. Random sampling, sufficient sample quantity, careful examination and taking history, improving examination rate, accurate diagnosis, strict training and preliminary study, as well as quality control can eliminate or minimize biases and improve the sampling survey quality of eye diseases in China

  18. Bias in air sampling techniques used to measure inhalation exposure

    SciTech Connect

    Cohen, B.S.; Harley, N.H.; Lippmann, M.

    1984-03-01

    Factors have been evaluated which contribute to the lack of agreement between inhalation exposure estimates obtained by time-weighted averaging of samples taken with mini hi-volume samplers, and those measured by time integrating, low-volume, lapel mounted, personal monitors. Measurements made with real-time aerosol monitors on workers at a Be-Cu production furnace show that part of the discrepancy results from variability of the aerosol concentration within the breathing zone. Field studies of sampler inlet bias, the influences of the electrostatic fields around polystyrene filter holders, and resuspension of dust from work clothing, were done in three areas of a Be plant. No significant differences were found in Be air concentrations measured simultaneously by open and closed face cassettes, and mini hi-volume samplers mounted on a test stand. No significant influence on Be collection was detected between either positively or negatively charged monitors and charge neutralized control monitors. The effect of contaminated work clothing on dust collection by lapel mounted monitors is most important. Beryllium release from the fabrics affected air concentrations measured by fabric mounted monitors more than it affected concentrations measured by monitors positioned above the fabrics. The latter were placed 16 cm from the vertically mounted fabrics, to simulate the position of the nose or mouth. The authors conclude that dust resuspended from work clothing is the major source of the observed discrepancy between exposures estimated from lapel mounted samplers and time-weighted averages.

  19. Combining reactive and configurational-bias Monte Carlo: Confinement influence on the propene metathesis reaction system in various zeolites

    NASA Astrophysics Data System (ADS)

    Jakobtorweihen, S.; Hansen, N.; Keil, F. J.

    2006-12-01

    In order to efficiently calculate chemical equilibria of large molecules in a confined environment the reactive Monte Carlo technique is combined with the configurational-bias Monte Carlo approach. To prove that detailed balance is fulfilled the acceptance rule for this combination of particular Monte Carlo techniques is derived in detail. Notably, by using this derivation all other acceptance rules of any Monte Carlo trial moves usually carried out in combination with the configurational-bias Monte Carlo approach can be deduced from it. As an application of the combination of reactive and configurational-bias Monte Carlo the influence of different zeolitic confinements (MFI, TON, LTL, and FER) on the reaction equilibrium and the selectivity of the propene metathesis reaction system was investigated. Compared to the bulk phase the conversion is increased significantly. The authors study this reaction system in the temperature range between 300 and 600K, and the pressure range from 1to7bars. In contrast to the bulk phase, pressure and temperature have a strong influence on the composition of the reaction mixture in confinement. At low pressures and temperatures both conversion and selectivity are highest. Furthermore, the equilibrium composition is strongly dependent on the type of zeolite. This demonstrates the important role of the host structure in catalytic systems.

  20. Using stochastic sampling of parametric uncertainties to quantify relationships between CAM3.1 bias and climate sensitivity

    NASA Astrophysics Data System (ADS)

    Jackson, C. S.; Tobis, M.

    2011-12-01

    It is an untested assumption in climate model evaluation that climate model biases affect its credibility. Models with the smaller biases are often regarded as being more plausible than models with larger biases. However not all biases affect predictions. It is only those biases that are involved with feedback mechanisms can lead to scatter in its predictions of change. To date no metric of model skill has been defined that can predict a model's sensitivity greenhouse gas forcing. Being able to do so will be an important step to how we can use observations to define a model's credibility. We shall present results of a calculation in which we attempt to isolate the contribution of errors in particular regions and fields to uncertainties in CAM3.1 equilibrium sensitivity to a doubling of CO2 forcing. In this calculation, observations, Bayesian inference, and stochastic sampling are used to identify a large ensemble of CAM3.1 configurations that represent uncertainties in selecting 15 model parameters important to clouds, convection, and radiation. A slab ocean configuration of CAM3.1 is then used to estimate the effects of these parametric uncertainties on projections of global warming through its equilibrium response to 2 x CO2 forcing. We then correlate the scatter in the control climate at each grid point and field to the scatter in climate sensitivities. The presentation will focus on the analysis of these results.

  1. Configurations and calibration methods for passive sampling techniques.

    PubMed

    Ouyang, Gangfeng; Pawliszyn, Janusz

    2007-10-19

    Passive sampling technology has developed very quickly in the past 15 years, and is widely used for the monitoring of pollutants in different environments. The design and quantification of passive sampling devices require an appropriate calibration method. Current calibration methods that exist for passive sampling, including equilibrium extraction, linear uptake, and kinetic calibration, are presented in this review. A number of state-of-the-art passive sampling devices that can be used for aqueous and air monitoring are introduced according to their calibration methods.

  2. Construction of and efficient sampling from the simplicial configuration model

    NASA Astrophysics Data System (ADS)

    Young, Jean-Gabriel; Petri, Giovanni; Vaccarino, Francesco; Patania, Alice

    2017-09-01

    Simplicial complexes are now a popular alternative to networks when it comes to describing the structure of complex systems, primarily because they encode multinode interactions explicitly. With this new description comes the need for principled null models that allow for easy comparison with empirical data. We propose a natural candidate, the simplicial configuration model. The core of our contribution is an efficient and uniform Markov chain Monte Carlo sampler for this model. We demonstrate its usefulness in a short case study by investigating the topology of three real systems and their randomized counterparts (using their Betti numbers). For two out of three systems, the model allows us to reject the hypothesis that there is no organization beyond the local scale.

  3. An experimental verification of laser-velocimeter sampling bias and its correction

    NASA Technical Reports Server (NTRS)

    Johnson, D. A.; Modarress, D.; Owen, F. K.

    1982-01-01

    The existence of 'sampling bias' in individual-realization laser velocimeter measurements is experimentally verified and shown to be independent of sample rate. The experiments were performed in a simple two-stream mixing shear flow with the standard for comparison being laser-velocimeter results obtained under continuous-wave conditions. It is also demonstrated that the errors resulting from sampling bias can be removed by a proper interpretation of the sampling statistics. In addition, data obtained in a shock-induced separated flow and in the near-wake of airfoils are presented, both bias-corrected and uncorrected, to illustrate the effects of sampling bias in the extreme.

  4. Shock-induced explosive chemistry in a deterministic sample configuration.

    SciTech Connect

    Stuecker, John Nicholas; Castaneda, Jaime N.; Cesarano, Joseph, III; Trott, Wayne Merle; Baer, Melvin R.; Tappan, Alexander Smith

    2005-10-01

    Explosive initiation and energy release have been studied in two sample geometries designed to minimize stochastic behavior in shock-loading experiments. These sample concepts include a design with explosive material occupying the hole locations of a close-packed bed of inert spheres and a design that utilizes infiltration of a liquid explosive into a well-defined inert matrix. Wave profiles transmitted by these samples in gas-gun impact experiments have been characterized by both velocity interferometry diagnostics and three-dimensional numerical simulations. Highly organized wave structures associated with the characteristic length scales of the deterministic samples have been observed. Initiation and reaction growth in an inert matrix filled with sensitized nitromethane (a homogeneous explosive material) result in wave profiles similar to those observed with heterogeneous explosives. Comparison of experimental and numerical results indicates that energetic material studies in deterministic sample geometries can provide an important new tool for validation of models of energy release in numerical simulations of explosive initiation and performance.

  5. Mars Rover Sample Return aerocapture configuration design and packaging constraints

    NASA Technical Reports Server (NTRS)

    Lawson, Shelby J.

    1989-01-01

    This paper discusses the aerodynamics requirements, volume and mass constraints that lead to a biconic aeroshell vehicle design that protects the Mars Rover Sample Return (MRSR) mission elements from launch to Mars landing. The aerodynamic requirements for Mars aerocapture and entry and packaging constraints for the MRSR elements result in a symmetric biconic aeroshell that develops a L/D of 1.0 at 27.0 deg angle of attack. A significant problem in the study is obtaining a cg that provides adequate aerodynamic stability and performance within the mission imposed constraints. Packaging methods that relieve the cg problems include forward placement of aeroshell propellant tanks and incorporating aeroshell structure as lander structure. The MRSR missions developed during the pre-phase A study are discussed with dimensional and mass data included. Further study is needed for some missions to minimize MRSR element volume so that launch mass constraints can be met.

  6. Mars Rover Sample Return aerocapture configuration design and packaging constraints

    NASA Technical Reports Server (NTRS)

    Lawson, Shelby J.

    1989-01-01

    This paper discusses the aerodynamics requirements, volume and mass constraints that lead to a biconic aeroshell vehicle design that protects the Mars Rover Sample Return (MRSR) mission elements from launch to Mars landing. The aerodynamic requirements for Mars aerocapture and entry and packaging constraints for the MRSR elements result in a symmetric biconic aeroshell that develops a L/D of 1.0 at 27.0 deg angle of attack. A significant problem in the study is obtaining a cg that provides adequate aerodynamic stability and performance within the mission imposed constraints. Packaging methods that relieve the cg problems include forward placement of aeroshell propellant tanks and incorporating aeroshell structure as lander structure. The MRSR missions developed during the pre-phase A study are discussed with dimensional and mass data included. Further study is needed for some missions to minimize MRSR element volume so that launch mass constraints can be met.

  7. Empirical Validation of a Procedure to Correct Position and Stimulus Biases in Matching-to-Sample

    ERIC Educational Resources Information Center

    Kangas, Brian D.; Branch, Marc N.

    2008-01-01

    The development of position and stimulus biases often occurs during initial training on matching-to-sample tasks. Furthermore, without intervention, these biases can be maintained via intermittent reinforcement provided by matching-to-sample contingencies. The present study evaluated the effectiveness of a correction procedure designed to…

  8. A smile biases the recognition of eye expressions: configural projection from a salient mouth.

    PubMed

    Calvo, Manuel G; Fernández-Martín, Andrés; Nummenmaa, Lauri

    2013-06-01

    A smile is visually highly salient and grabs attention automatically. We investigated how extrafoveally seen smiles influence the viewers' perception of non-happy eyes in a face. A smiling mouth appeared in composite faces with incongruent non-happy (fearful, neutral, etc.) eyes, thus producing blended expressions, or it appeared in intact faces with genuine expressions. Attention to the eye region was spatially cued while foveal vision of the mouth was blocked by gaze-contingent masking. Participants judged whether the eyes were happy or not. Results indicated that the smile biased the evaluation of the eye expression: The same non-happy eyes were more likely to be judged as happy and categorized more slowly as not happy in a face with a smiling mouth than in a face with a non-smiling mouth or with no mouth. This bias occurred when the mouth and the eyes appeared simultaneously and aligned, but also to some extent when they were misaligned and when the mouth appeared after the eyes. We conclude that the highly salient smile projects to other facial regions, thus influencing the perception of the eye expression. Projection serves spatial and temporal integration of face parts and changes.

  9. Spin-torque driven magnetization switching in ferromagnetic nanopillar with pinned layer biasing configuration

    SciTech Connect

    Bhoomeeswaran, H.; Sabareesan, P.; Bharathi, B. Divya

    2016-05-06

    Magnetization switching driven by spin transfer torque in a ferromagnetic nanopillar by biasing the angular polarizer with different orientation has been studied. The free layer dynamics includes the spin torque from the oscillating free layer with magneto crystalline anisotropy and shape anisotropy, which is governed by the Landau-Lifshitsz-Gilbert-Slonczweski (LLGS) equation and solving it numerically by using embedded Runge Kutta fourth order method. Results of numerical simulation shows that there is a drastic reduction of switching time in the free layer by the orientation of angular polarizer of the nano pillar device. We fixed the angular polarizer as 0°, 30°, 60°, 90° and the corresponding switching time is 6.53 ns, 4.36 ns, 2.25 ns and 1.21 ns respectively for an applied current density of 5 × 10{sup 11} Am{sup −2}.

  10. Bias due to participant overlap in two‐sample Mendelian randomization

    PubMed Central

    Davies, Neil M.; Thompson, Simon G.

    2016-01-01

    ABSTRACT Mendelian randomization analyses are often performed using summarized data. The causal estimate from a one‐sample analysis (in which data are taken from a single data source) with weak instrumental variables is biased in the direction of the observational association between the risk factor and outcome, whereas the estimate from a two‐sample analysis (in which data on the risk factor and outcome are taken from non‐overlapping datasets) is less biased and any bias is in the direction of the null. When using genetic consortia that have partially overlapping sets of participants, the direction and extent of bias are uncertain. In this paper, we perform simulation studies to investigate the magnitude of bias and Type 1 error rate inflation arising from sample overlap. We consider both a continuous outcome and a case‐control setting with a binary outcome. For a continuous outcome, bias due to sample overlap is a linear function of the proportion of overlap between the samples. So, in the case of a null causal effect, if the relative bias of the one‐sample instrumental variable estimate is 10% (corresponding to an F parameter of 10), then the relative bias with 50% sample overlap is 5%, and with 30% sample overlap is 3%. In a case‐control setting, if risk factor measurements are only included for the control participants, unbiased estimates are obtained even in a one‐sample setting. However, if risk factor data on both control and case participants are used, then bias is similar with a binary outcome as with a continuous outcome. Consortia releasing publicly available data on the associations of genetic variants with continuous risk factors should provide estimates that exclude case participants from case‐control samples. PMID:27625185

  11. Characteristics of interpretation bias and relationship with suicidality in a psychiatric hospital sample.

    PubMed

    Beard, Courtney; Rifkin, Lara S; Björgvinsson, Thröstur

    2017-01-01

    Interpretation bias, the tendency to interpret ambiguous situations negatively (or to lack a positive bias), is a cognitive vulnerability associated with psychopathology. However, there is a lack of research characterizing this bias in psychiatric samples, including whether it is also a risk factor for suicidality. This study characterized interpretation bias in a psychiatric sample at risk for suicide and examined the relationship between interpretation bias and suicidality cross-sectionally and prospectively. Patients (N=65) attending a partial hospital program completed the Word-Sentence Association Paradigm (WSAP), which results in four variables reflecting different types of interpretation bias: endorsement rates and reaction time bias scores for negative and benign interpretations. We conducted logistic regression models to predict high suicidality (ideation, plans, attempts, etc. assessed via a structured interview at admission) and suicidal ideation (assessed via self-report at admission and discharge). Logistic regression models predicting suicide outcomes upon admission and discharge indicated that benign interpretation endorsement was the most robust predictor of suicidality concurrently and prospectively, controlling for baseline suicidal ideation. Lack of gold standard self-report suicide assessment. Unable to assess additional constructs such as hopelessness or perfectionism, which may better elucidate how lacking a benign bias influences suicidality. Modest sample size. A lower endorsement of positive interpretations was the strongest predictor of prospective suicidal ideation, even after controlling for baseline suicidal ideation. Future research should examine how targeting interpretation bias influences suicidality. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Is Knowledge Random? Introducing Sampling and Bias through Outdoor Inquiry

    ERIC Educational Resources Information Center

    Stier, Sam

    2010-01-01

    Sampling, very generally, is the process of learning about something by selecting and assessing representative parts of that population or object. In the inquiry activity described here, students learned about sampling techniques as they estimated the number of trees greater than 12 cm dbh (diameter at breast height) in a wooded, discrete area…

  13. Commingled Samples: A Neglected Source of Bias in Reliability Analysis

    ERIC Educational Resources Information Center

    Waller, Niels G.

    2008-01-01

    Reliability is a property of test scores from individuals who have been sampled from a well-defined population. Reliability indices, such as coefficient and related formulas for internal consistency reliability (KR-20, Hoyt's reliability), yield lower bound reliability estimates when (a) subjects have been sampled from a single population and when…

  14. Is Knowledge Random? Introducing Sampling and Bias through Outdoor Inquiry

    ERIC Educational Resources Information Center

    Stier, Sam

    2010-01-01

    Sampling, very generally, is the process of learning about something by selecting and assessing representative parts of that population or object. In the inquiry activity described here, students learned about sampling techniques as they estimated the number of trees greater than 12 cm dbh (diameter at breast height) in a wooded, discrete area…

  15. Variable selection and prediction in biased samples with censored outcomes.

    PubMed

    Wu, Ying; Cook, Richard J

    2017-02-18

    With the increasing availability of large prospective disease registries, scientists studying the course of chronic conditions often have access to multiple data sources, with each source generated based on its own entry conditions. The different entry conditions of the various registries may be explicitly based on the response process of interest, in which case the statistical analysis must recognize the unique truncation schemes. Moreover, intermittent assessment of individuals in the registries can lead to interval-censored times of interest. We consider the problem of selecting important prognostic biomarkers from a large set of candidates when the event times of interest are truncated and right- or interval-censored. Methods for penalized regression are adapted to handle truncation via a Turnbull-type complete data likelihood. An expectation-maximization algorithm is described which is empirically shown to perform well. Inverse probability weights are used to adjust for the selection bias when assessing predictive accuracy based on individuals whose event status is known at a time of interest. Application to the motivating study of the development of psoriatic arthritis in patients with psoriasis in both the psoriasis cohort and the psoriatic arthritis cohort illustrates the procedure.

  16. Identification of potential biases in the characterization sampling and analysis process

    SciTech Connect

    Winkelman, W.D.; Eberlein, S.J.

    1995-12-01

    The Tank Waste Remediation System (TWRS) Characterization Project is responsible for providing quality characterization data to TWRS. Documentation of sampling and analysis process errors and biases can be used to improve the process to provide that data. The sampling and analysis process consists of removing a sample from a specified waste tank, getting it to the laboratory and analyzing it to provide the data identified in the Tank Characterization Plan (TCP) and Sampling and Analysis Plan (SAP). To understand the data fully, an understanding of errors or biases that can be generated during the process is necessary. Most measurement systems have the ability statistically to detect errors and biases by using standards and alternate measurement techniques. Only the laboratory analysis part of the tank sampling and analysis process at TWRS has this ability. Therefore, it is necessary to use other methods to identify and prioritize the biases involved in the process.

  17. Assessment and Optimization of Configurational-Bias Monte Carlo Particle Swap Strategies for Simulations of Water in the Gibbs Ensemble.

    PubMed

    Bai, Peng; Siepmann, J Ilja

    2017-02-14

    Particle swap moves between phases are usually the rate-limiting step for Gibbs ensemble Monte Carlo (GEMC) simulations of fluid phase equilibria at low reduced temperatures because the acceptance probabilities for these moves can become very low for molecules with articulated architecture and/or highly directional interactions. The configurational-bias Monte Carlo (CBMC) technique can greatly increase the acceptance probabilities, but the efficiency of the CBMC algorithm is influenced by multiple parameters. In this work we assess the performance of different CBMC strategies for GEMC simulations using the SPC/E and TIP4P water models at 283, 343, and 473 K, demonstrate that much higher acceptance probabilities can be achieved than previously reported in the literature, and make recommendations for CBMC strategies leading to optimal efficiency.

  18. Estimating the occupancy of spotted owl habitat areas by sampling and adjusting for bias

    Treesearch

    David L. Azuma; James A. Baldwin; Barry R. Noon

    1990-01-01

    A basic sampling scheme is proposed to estimate the proportion of sampled units (Spotted Owl Habitat Areas (SOHAs) or randomly sampled 1000-acre polygon areas (RSAs)) occupied by spotted owl pairs. A bias adjustment for the possibility of missing a pair given its presence on a SOHA or RSA is suggested. The sampling scheme is based on a fixed number of visits to a...

  19. Biased Sampling and PCK: The Case of the Marijuana Problem

    ERIC Educational Resources Information Center

    Watson, Jane M.; Nathan, Erica L.

    2010-01-01

    As part of an interview protocol investigating teachers' pedagogical content knowledge (PCK) in statistics, 40 teachers were presented with a newspaper article reporting a phone-in survey about the legalisation of marijuana. The article and a question about the reliability of the sample had earlier been used in student surveys, and three student…

  20. A “Scientific Diversity” Intervention to Reduce Gender Bias in a Sample of Life Scientists

    PubMed Central

    Moss-Racusin, Corinne A.; van der Toorn, Jojanneke; Dovidio, John F.; Brescoll, Victoria L.; Graham, Mark J.; Handelsman, Jo

    2016-01-01

    Mounting experimental evidence suggests that subtle gender biases favoring men contribute to the underrepresentation of women in science, technology, engineering, and mathematics (STEM), including many subfields of the life sciences. However, there are relatively few evaluations of diversity interventions designed to reduce gender biases within the STEM community. Because gender biases distort the meritocratic evaluation and advancement of students, interventions targeting instructors’ biases are particularly needed. We evaluated one such intervention, a workshop called “Scientific Diversity” that was consistent with an established framework guiding the development of diversity interventions designed to reduce biases and was administered to a sample of life science instructors (N = 126) at several sessions of the National Academies Summer Institute for Undergraduate Education held nationwide. Evidence emerged indicating the efficacy of the “Scientific Diversity” workshop, such that participants were more aware of gender bias, expressed less gender bias, and were more willing to engage in actions to reduce gender bias 2 weeks after participating in the intervention compared with 2 weeks before the intervention. Implications for diversity interventions aimed at reducing gender bias and broadening the participation of women in the life sciences are discussed. PMID:27496360

  1. A "Scientific Diversity" Intervention to Reduce Gender Bias in a Sample of Life Scientists.

    PubMed

    Moss-Racusin, Corinne A; van der Toorn, Jojanneke; Dovidio, John F; Brescoll, Victoria L; Graham, Mark J; Handelsman, Jo

    2016-01-01

    Mounting experimental evidence suggests that subtle gender biases favoring men contribute to the underrepresentation of women in science, technology, engineering, and mathematics (STEM), including many subfields of the life sciences. However, there are relatively few evaluations of diversity interventions designed to reduce gender biases within the STEM community. Because gender biases distort the meritocratic evaluation and advancement of students, interventions targeting instructors' biases are particularly needed. We evaluated one such intervention, a workshop called "Scientific Diversity" that was consistent with an established framework guiding the development of diversity interventions designed to reduce biases and was administered to a sample of life science instructors (N = 126) at several sessions of the National Academies Summer Institute for Undergraduate Education held nationwide. Evidence emerged indicating the efficacy of the "Scientific Diversity" workshop, such that participants were more aware of gender bias, expressed less gender bias, and were more willing to engage in actions to reduce gender bias 2 weeks after participating in the intervention compared with 2 weeks before the intervention. Implications for diversity interventions aimed at reducing gender bias and broadening the participation of women in the life sciences are discussed.

  2. Bias in groundwater samples caused by wellbore flow

    USGS Publications Warehouse

    Reilly, Thomas E.; Franke, O. Lehn; Bennett, Gordon D.

    1989-01-01

    Proper design of physical installations and sampling procedures for groundwater monitoring networks is critical for the detection and analysis of possible contaminants. Monitoring networks associated with known contaminant sources sometimes include an array of monitoring wells with long well screens. The purpose of this paper is: (a) to report the results of a numerical experiment indicating that significant borehole flow can occur within long well screens installed in homogeneous aquifers with very small head differences in the aquifer (less than 0.01 feet between the top and bottom of the screen); (b) to demonstrate that contaminant monitoring wells with long screens may completely fail to fulfill their purpose in many groundwater environments.

  3. Evaluation of different synchrotron beamline configurations for X-ray fluorescence analysis of environmental samples.

    PubMed

    Barberie, Sean R; Iceman, Christopher R; Cahill, Catherine F; Cahill, Thomas M

    2014-08-19

    Synchrotron radiation X-ray fluorescence (SR-XRF) is a powerful elemental analysis tool, yet synchrotrons are large, multiuser facilities that are generally not amenable to modification. However, the X-ray beamlines from synchrotrons can be modified by simply including X-ray filters or removing monochromators to improve the SR-XRF analysis. In this study, we evaluated four easily applied beamline configurations for the analysis of three representative environmental samples, namely a thin aerosol sample, an intermediate thickness biological sample, and a thick rare earth mineral specimen. The results showed that the "white beam" configuration, which was simply the full, polychromatic output of the synchrotron, was the optimal configuration for the analysis of thin samples with little mass. The "filtered white beam" configuration removed the lower energy X-rays from the excitation beam so it gave better sensitivity for elements emitting more energetic X-rays. The "filtered white beam-filtered detector" configuration sacrifices the lower energy part of the spectrum (<15 keV) for improved sensitivity in the higher end (∼26 to 48 keV range). The use of a monochromatic beam, which tends to be the standard mode of operation for most SR-XRF analyses reported in the literature, gave the least sensitive analysis.

  4. Investigation of reflectance sampling depth in biological tissues for various common illumination/collection configurations.

    PubMed

    Zonios, George

    2014-09-01

    Knowledge of light penetration characteristics is very important in almost all studies in biomedical optics. In this work, the reflectance sampling depth in biological tissues was investigated using Monte Carlo simulations for various common illumination/collection configurations. The analysis shows that the average sampling depth can be described by two simple empirical analytical expressions over the entire typical ranges of absorption and scattering properties relevant to in vivo biological tissue, regardless of the specific illumination/collection configuration details. These results are promising and helpful for the quick, efficient, and accurate design of reflectance studies for various biological tissue applications.

  5. Sampling bias in an international internet survey of diversion programs in the criminal justice system.

    PubMed

    Hartford, Kathleen; Carey, Robert; Mendonca, James

    2007-03-01

    Despite advances in the storage and retrieval of information within health care systems, health researchers conducting surveys for evaluations still face technical barriers that may lead to sampling bias. The authors describe their experience in administering a Web-based, international survey to English-speaking countries. Identifying the sample was a multistage effort involving (a) searching for published e-mail addresses, (b) conducting Web searches for publicly funded agencies, and (c) performing literature searches, personal contacts, and extensive Internet searches for individuals. After pretesting, the survey was converted into an electronic format accessible by multiple Web browsers. Sampling bias arose from (a) system incompatibility, which did not allow potential respondents to open the survey, (b) varying institutional gate-keeping policies that "recognized" the unsolicited survey as spam, (c) culturally unique program terminology, which confused some respondents, and (d) incomplete sampling frames. Solutions are offered to the first three problems, and the authors note that sampling bias remains a crucial problem.

  6. Taken last, selected first: the sampling bias is also present in the haptic domain.

    PubMed

    Mitsuda, Takashi; Yoshioka, Yuichi

    2015-04-01

    When people are presented with a pair of images and asked to identify which one is more attractive, their eye gaze shifts gradually toward the image that they eventually choose. This study examined whether this sampling bias also occurs in other sensory modalities by observing participants' behavior in a haptic preference task. The results indicated that the participants tended to sample the chosen item just prior to making their decision when they were instructed to identify their most preferred item (i.e., the "like" task), but not when they were instructed to identify their least preferred item (i.e., the "dislike" task). This indicates that the sampling bias is a general phenomenon regardless of sensory modality. In addition, the sampling bias in the like task was larger when the difference in preference ratings between the paired items was smaller. However, the sampling bias decreased when the two items were given equal preference ratings, despite there being a longer decision time on those trials. This suggests that the sampling bias is not simply related to task difficulty, but is also related to preference formation and/or selective encoding of task-relevant information.

  7. Avoiding treatment bias of REDD+ monitoring by sampling with partial replacement.

    PubMed

    Köhl, Michael; Scott, Charles T; Lister, Andrew J; Demon, Inez; Plugge, Daniel

    2015-12-01

    Implementing REDD+ renders the development of a measurement, reporting and verification (MRV) system necessary to monitor carbon stock changes. MRV systems generally apply a combination of remote sensing techniques and in-situ field assessments. In-situ assessments can be based on 1) permanent plots, which are assessed on all successive occasions, 2) temporary plots, which are assessed only once, and 3) a combination of both. The current study focuses on in-situ assessments and addresses the effect of treatment bias, which is introduced by managing permanent sampling plots differently than the surrounding forests. Temporary plots are not subject to treatment bias, but are associated with large sampling errors and low cost-efficiency. Sampling with partial replacement (SPR) utilizes both permanent and temporary plots. We apply a scenario analysis with different intensities of deforestation and forest degradation to show that SPR combines cost-efficiency with the handling of treatment bias. Without treatment bias permanent plots generally provide lower sampling errors for change estimates than SPR and temporary plots, but do not provide reliable estimates, if treatment bias occurs, SPR allows for change estimates that are comparable to those provided by permanent plots, offers the flexibility to adjust sample sizes in the course of time, and allows to compare data on permanent versus temporary plots for detecting treatment bias. Equivalence of biomass or carbon stock estimates between permanent and temporary plots serves as an indication for the absence of treatment bias while differences suggest that there is evidence for treatment bias. SPR is a flexible tool for estimating emission factors from successive measurements. It does not entirely depend on sample plots that are installed at the first occasion but allows for the adjustment of sample sizes and placement of new plots at any occasion. This ensures that in-situ samples provide representative estimates over

  8. Test Equating from Biased Samples, with Application to the Armed Services Vocational Aptitude Battery.

    ERIC Educational Resources Information Center

    Little, Roderick J. A.; Rubin, Donald B.

    1994-01-01

    Equating a new standard test to an old reference test is considered when samples for equating are not randomly selected from the target population of test takers, identifying two problems from equating from biased samples. An empirical example with data from the Armed Services Vocational Aptitude Battery illustrates the approach. (SLD)

  9. Calculating sample size for studies with expected all-or-none nonadherence and selection bias.

    PubMed

    Shardell, Michelle D; El-Kamary, Samer S

    2009-06-01

    We develop sample size formulas for studies aiming to test mean differences between a treatment and control group when all-or-none nonadherence (noncompliance) and selection bias are expected. Recent work by Fay, Halloran, and Follmann (2007, Biometrics 63, 465-474) addressed the increased variances within groups defined by treatment assignment when nonadherence occurs, compared to the scenario of full adherence, under the assumption of no selection bias. In this article, we extend the authors' approach to allow selection bias in the form of systematic differences in means and variances among latent adherence subgroups. We illustrate the approach by performing sample size calculations to plan clinical trials with and without pilot adherence data. Sample size formulas and tests for normally distributed outcomes are also developed in a Web Appendix that account for uncertainty of estimates from external or internal pilot data.

  10. Calculating Sample Size for Studies with Expected All-or-None Nonadherence and Selection Bias

    PubMed Central

    Shardell, Michelle D.; El-Kamary, Samer S.

    2015-01-01

    Summary We develop sample size formulas for studies aiming to test mean differences between a treatment and control group when all-or-none nonadherence (noncompliance) and selection bias are expected. Recent work addressed the increased variances within groups defined by treatment assignment when nonadherence occurs, compared to the scenario of full adherence, under the assumption of no selection bias. In this article, we extend the authors’ approach to allow selection bias in the form of systematic differences in means and variances among latent adherence subgroups. We illustrate the approach by performing sample size calculations to plan clinical trials with and without pilot adherence data. Sample size formulas and tests for normally distributed outcomes are also developed in a Web Appendix that account for uncertainty of estimates from external or internal pilot data. PMID:18759830

  11. A likelihood perspective on tree-ring standardization: eliminating modern sample bias

    NASA Astrophysics Data System (ADS)

    Cecile, J.; Pagnutti, C.; Anand, M.

    2013-08-01

    It has recently been suggested that non-random sampling and differences in mortality between trees of different growth rates is responsible for a widespread, systematic bias in dendrochronological reconstructions of tree growth known as modern sample bias. This poses a serious challenge for climate reconstruction and the detection of long-term changes in growth. Explicit use of growth models based on regional curve standardization allow us to investigate the effects on growth due to age (the regional curve), year (the standardized chronology or forcing) and a new effect, the productivity of each tree. Including a term for the productivity of each tree accounts for the underlying cause of modern sample bias, allowing for more reliable reconstruction of low-frequency variability in tree growth. This class of models describes a new standardization technique, fixed effects standardization, that contains both classical regional curve standardization and flat detrending. Signal-free standardization accounts for unbalanced experimental design and fits the same growth model as classical least-squares or maximum likelihood regression techniques. As a result, we can use powerful and transparent tools such as R2 and Akaike's Information Criteria to assess the quality of tree ring standardization, allowing for objective decisions between competing techniques. Analyzing 1200 randomly selected published chronologies, we find that regional curve standardization is improved by adding an effect for individual tree productivity in 99% of cases, reflecting widespread differing-contemporaneous-growth rate bias. Furthermore, modern sample bias produced a significant negative bias in estimated tree growth by time in 70.5% of chronologies and a significant positive bias in 29.5% of chronologies. This effect is largely concentrated in the last 300 yr of growth data, posing serious questions about the homogeneity of modern and ancient chronologies using traditional standardization

  12. Systematic approach to conformational sampling for assigning absolute configuration using vibrational circular dichroism.

    PubMed

    Sherer, Edward C; Lee, Claire H; Shpungin, Joseph; Cuff, James F; Da, Chenxiao; Ball, Richard; Bach, Richard; Crespo, Alejandro; Gong, Xiaoyi; Welch, Christopher J

    2014-01-23

    Systematic methods that speed-up the assignment of absolute configuration using vibrational circular dichrosim (VCD) and simplify its usage will advance this technique into a robust platform technology. Applying VCD to pharmaceutically relevant compounds has been handled in an ad hoc fashion, relying on fragment analysis and technical shortcuts to reduce the computational time required. We leverage a large computational infrastructure to provide adequate conformational exploration which enables an accurate assignment of absolute configuration. We describe a systematic approach for rapid calculation of VCD/IR spectra and comparison with corresponding measured spectra and apply this approach to assign the correct stereochemistry of nine test cases. We suggest moving away from the fragment approach when making VCD assignments. In addition to enabling faster and more reliable VCD assignments of absolute configuration, the ability to rapidly explore conformational space and sample conformations of complex molecules will have applicability in other areas of drug discovery.

  13. On the efficiency of biased sampling of the multiple state path ensemble

    NASA Astrophysics Data System (ADS)

    Rogal, Jutta; Bolhuis, Peter G.

    2010-07-01

    Developed for complex systems undergoing rare events involving many (meta)stable states, the multiple state transition path sampling aims to sample from an extended path ensemble including all possible trajectories between any pair of (meta)stable states. The key issue for an efficient sampling of the path space in this extended ensemble is sufficient switching between different types of trajectories. When some transitions are much more likely than others the collective sampling of the different path types can become difficult. Here we introduce a Wang-Landau based biasing approach to improve the sampling. We find that the biasing of the multiple state path ensemble does not influence the switching behavior, but does improve the sampling and thus the quality of the individual path ensembles.

  14. Sampling Biases in MODIS and SeaWiFS Ocean Chlorophyll Data

    NASA Technical Reports Server (NTRS)

    Gregg, Watson W.; Casey, Nancy W.

    2007-01-01

    Although modem ocean color sensors, such as MODIS and SeaWiFS are often considered global missions, in reality it takes many days, even months, to sample the ocean surface enough to provide complete global coverage. The irregular temporal sampling of ocean color sensors can produce biases in monthly and annual mean chlorophyll estimates. We quantified the biases due to sampling using data assimilation to create a "truth field", which we then sub-sampled using the observational patterns of MODIS and SeaWiFS. Monthly and annual mean chlorophyll estimates from these sub-sampled, incomplete daily fields were constructed and compared to monthly and annual means from the complete daily fields of the assimilation model, at a spatial resolution of 1.25deg longitude by 0.67deg latitude. The results showed that global annual mean biases were positive, reaching nearly 8% (MODIS) and >5% (SeaWiFS). For perspective the maximum interannual variability in the SeaWiFS chlorophyll record was about 3%. Annual mean sampling biases were low (<3%) in the midlatitudes (between -40deg and 40deg). Low interannual variability in the global annual mean sampling biases suggested that global scale trend analyses were valid. High latitude biases were much higher than the global annual means, up to 20% as a basin annual mean, and over 80% in some months. This was the result of the high solar zenith angle exclusion in the processing algorithms. Only data where the solar angle is <75deg are permitted, in contrast to the assimilation which samples regularly over the entire area and month. High solar zenith angles do not facilitate phytoplankton photosynthesis and consequently low chlorophyll concentrations occurring here are missed by the data sets. Ocean color sensors selectively sample in locations and times of favorable phytoplankton growth, producing overestimates of chlorophyll. The biases derived from lack of sampling in the high latitudes varied monthly, leading to artifacts in the apparent

  15. Bias correction of EU-ENSEMBLES precipitation data with focus on the effect of sample size

    NASA Astrophysics Data System (ADS)

    Reiter, Philipp; Gutjahr, Oliver; Schefczyk, Lukas; Heinemann, Günther; Casper, Markus C.

    2015-04-01

    The precipitation output of climate models often shows a bias when compared to observed data, so that a bias correction is necessary before using it as climate forcing in impact modeling. We expect the performance of the bias correction to strongly depend on the sample size used for its calibration. This raises the question: how long does a time series need to be to achieve a sufficient bias correction? We carry out experiments using 40 years of daily precipitation data from 10 regional climate models (RCM) of the EU-ENSEMBLES project, splitting them into a 30 year calibration period and a 10 year validation period. The RCM data are bias corrected using decreasing sample sizes out of the calibration period. By applying skill scores we quantify the critical sample size ncrit, at which the quality of the bias correction becomes statistically worse compared to the correction based on 30 years. In order to analyze whether the effect of the sample size depends on the chosen correction method and the calibration period, we applied four variations of the quantile matching (QM) approach and 3 different calibration/validation periods in this study. The results show that the spread of ncrit is large, ranging from 28 years to approximately 10 years. This indicates that even a small decrease in sample size for the calibration can result in a statistical significant degradation of the bias correction. Corrections with sample sizes smaller than 10 years always perform significantly worse than the 'best fit' with 30 years. The chosen QM approach influences ncrit in dependence of its degrees of freedom: the higher the degrees of freedom the larger ncrit. We also found that the choice of the calibration period affects the ncrit values. In conclusion we recommend to use time series as long as possible for bias correction of precipitation data. However, there is a large transition zone of the critical sample size where shorter time series can perform sufficiently well, depending on

  16. Nonadherence with ambulatory saliva sampling is associated with biased salivary testosterone estimates.

    PubMed

    Moeller, Julian; Lieb, Roselind; Meyer, Andrea H; Quack Loetscher, Katharina; Krastel, Bettina; Meinlschmidt, Gunther

    2014-06-01

    Nonadherence with scheduled saliva sampling, as encountered in ambulatory settings, can bias the estimation of salivary cortisol concentrations. This study is the first to estimate if such nonadherence is also associated with biased salivary testosterone concentration estimates. Using a standard ambulatory saliva-sampling protocol, we instructed pregnant women to collect saliva samples on two consecutive days at awakening, 1100h, 1500h, 2000h, and 2200h. We estimated testosterone concentrations in the saliva samples and participants' actual sampling times with an electronic medication event-monitoring system. We classified a saliva sample as adherent if it was sampled within a specific time window relative to its scheduled sampling time. We used a mixed-model analysis to distinguish between trait (number of adherent saliva samples per participant) and state (adherence status of a specific sample) adherence. We included 60 pregnant women in this study. Seventy-five percent (448 of 600) of the scheduled samples indicated adherence with the sampling schedule. Participants' trait adherence was associated with their diurnal profiles of salivary testosterone estimates; that is, adherent participants had higher salivary testosterone estimates compared with nonadherent participants, F(1,58)=5.41, p=0.023, Cohen's d=0.67. The state adherence of a sample was associated with the salivary testosterone estimate of the related sample, F(1,469)=4.48, p=0.035, Cohen's d=0.20, with delayed sampling associated with lower salivary testosterone estimates. The results suggest that common ambulatory nonadherence with scheduled saliva sampling is associated with biased salivary testosterone estimates. They will inform further studies estimating salivary testosterone with ambulatory saliva-sampling designs and highlight the relevance of strategies to improve or confirm adherence, beyond routinely used instructions. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. Investigation of Particle Sampling Bias in the Shear Flow Field Downstream of a Backward Facing Step

    NASA Technical Reports Server (NTRS)

    Meyers, James F.; Kjelgaard, Scott O.; Hepner, Timothy E.

    1990-01-01

    The flow field about a backward facing step was investigated to determine the characteristics of particle sampling bias in the various flow phenomena. The investigation used the calculation of the velocity:data rate correlation coefficient as a measure of statistical dependence and thus the degree of velocity bias. While the investigation found negligible dependence within the free stream region, increased dependence was found within the boundary and shear layers. Full classic correction techniques over-compensated the data since the dependence was weak, even in the boundary layer and shear regions. The paper emphasizes the necessity to determine the degree of particle sampling bias for each measurement ensemble and not use generalized assumptions to correct the data. Further, it recommends the calculation of the velocity:data rate correlation coefficient become a standard statistical calculation in the analysis of all laser velocimeter data.

  18. Quantifying sample biases of inland lake sampling programs in relation to lake surface area and land use/cover.

    PubMed

    Wagner, Tyler; Soranno, Patricia A; Cheruvelil, Kendra Spence; Renwick, William H; Webster, Katherine E; Vaux, Peter; Abbitt, Robbyn J F

    2008-06-01

    We quantified potential biases associated with lakes monitored using non-probability based sampling by six state agencies in the USA (Michigan, Wisconsin, Iowa, Ohio, Maine, and New Hampshire). To identify biases, we compared state-monitored lakes to a census population of lakes derived from the National Hydrography Dataset. We then estimated the probability of lakes being sampled using generalized linear mixed models. Our two research questions were: (1) are there systematic differences in lake area and land use/land cover (LULC) surrounding lakes monitored by state agencies when compared to the entire population of lakes? and (2) after controlling for the effects of lake size, does the probability of sampling vary depending on the surrounding LULC features? We examined the biases associated with surrounding LULC because of the established links between LULC and lake water quality. For all states, we found that larger lakes had a higher probability of being sampled compared to smaller lakes. Significant interactions between lake size and LULC prohibit us from drawing conclusions about the main effects of LULC; however, in general lakes that are most likely to be sampled have either high urban use, high agricultural use, high forest cover, or low wetland cover. Our analyses support the assertion that data derived from non-probability-based surveys must be used with caution when attempting to make generalizations to the entire population of interest, and that probability-based surveys are needed to ensure unbiased, accurate estimates of lake status and trends at regional to national scales.

  19. Spatial recruitment bias in respondent-driven sampling: Implications for HIV prevalence estimation in urban heterosexuals.

    PubMed

    Jenness, Samuel M; Neaigus, Alan; Wendel, Travis; Gelpi-Acosta, Camila; Hagan, Holly

    2014-12-01

    Respondent-driven sampling (RDS) is a study design used to investigate populations for which a probabilistic sampling frame cannot be efficiently generated. Biases in parameter estimates may result from systematic non-random recruitment within social networks by geography. We investigate the spatial distribution of RDS recruits relative to an inferred social network among heterosexual adults in New York City in 2010. Mean distances between recruitment dyads are compared to those of network dyads to quantify bias. Spatial regression models are then used to assess the impact of spatial structure on risk and prevalence outcomes. In our primary distance metric, network dyads were an average of 1.34 (95 % CI 0.82–1.86) miles farther dispersed than recruitment dyads, suggesting spatial bias. However, there was no evidence that demographic associations with HIV risk or prevalence were spatially confounded. Therefore, while the spatial structure of recruitment may be biased in heterogeneous urban settings, the impact of this bias on estimates of outcome measures appears minimal.

  20. The second Southern African Bird Atlas Project: Causes and consequences of geographical sampling bias.

    PubMed

    Hugo, Sanet; Altwegg, Res

    2017-09-01

    Using the Southern African Bird Atlas Project (SABAP2) as a case study, we examine the possible determinants of spatial bias in volunteer sampling effort and how well such biased data represent environmental gradients across the area covered by the atlas. For each province in South Africa, we used generalized linear mixed models to determine the combination of variables that explain spatial variation in sampling effort (number of visits per 5' × 5' grid cell, or "pentad"). The explanatory variables were distance to major road and exceptional birding locations or "sampling hubs," percentage cover of protected, urban, and cultivated area, and the climate variables mean annual precipitation, winter temperatures, and summer temperatures. Further, we used the climate variables and plant biomes to define subsets of pentads representing environmental zones across South Africa, Lesotho, and Swaziland. For each environmental zone, we quantified sampling intensity, and we assessed sampling completeness with species accumulation curves fitted to the asymptotic Lomolino model. Sampling effort was highest close to sampling hubs, major roads, urban areas, and protected areas. Cultivated area and the climate variables were less important. Further, environmental zones were not evenly represented by current data and the zones varied in the amount of sampling required representing the species that are present. SABAP2 volunteers' preferences in birding locations cause spatial bias in the dataset that should be taken into account when analyzing these data. Large parts of South Africa remain underrepresented, which may restrict the kind of ecological questions that may be addressed. However, sampling bias may be improved by directing volunteers toward undersampled regions while taking into account volunteer preferences.

  1. Publication Bias in Psychology: A Diagnosis Based on the Correlation between Effect Size and Sample Size

    PubMed Central

    Kühberger, Anton; Fritz, Astrid; Scherndl, Thomas

    2014-01-01

    Background The p value obtained from a significance test provides no information about the magnitude or importance of the underlying phenomenon. Therefore, additional reporting of effect size is often recommended. Effect sizes are theoretically independent from sample size. Yet this may not hold true empirically: non-independence could indicate publication bias. Methods We investigate whether effect size is independent from sample size in psychological research. We randomly sampled 1,000 psychological articles from all areas of psychological research. We extracted p values, effect sizes, and sample sizes of all empirical papers, and calculated the correlation between effect size and sample size, and investigated the distribution of p values. Results We found a negative correlation of r = −.45 [95% CI: −.53; −.35] between effect size and sample size. In addition, we found an inordinately high number of p values just passing the boundary of significance. Additional data showed that neither implicit nor explicit power analysis could account for this pattern of findings. Conclusion The negative correlation between effect size and samples size, and the biased distribution of p values indicate pervasive publication bias in the entire field of psychology. PMID:25192357

  2. Publication bias in psychology: a diagnosis based on the correlation between effect size and sample size.

    PubMed

    Kühberger, Anton; Fritz, Astrid; Scherndl, Thomas

    2014-01-01

    The p value obtained from a significance test provides no information about the magnitude or importance of the underlying phenomenon. Therefore, additional reporting of effect size is often recommended. Effect sizes are theoretically independent from sample size. Yet this may not hold true empirically: non-independence could indicate publication bias. We investigate whether effect size is independent from sample size in psychological research. We randomly sampled 1,000 psychological articles from all areas of psychological research. We extracted p values, effect sizes, and sample sizes of all empirical papers, and calculated the correlation between effect size and sample size, and investigated the distribution of p values. We found a negative correlation of r = -.45 [95% CI: -.53; -.35] between effect size and sample size. In addition, we found an inordinately high number of p values just passing the boundary of significance. Additional data showed that neither implicit nor explicit power analysis could account for this pattern of findings. The negative correlation between effect size and samples size, and the biased distribution of p values indicate pervasive publication bias in the entire field of psychology.

  3. The use of volunteer radon measurements for radon mapping purposes: an examination of sampling bias issues.

    PubMed

    Burke, Orlaith; Murphy, Patrick

    2011-09-01

    National and regional radon surveys are used in many nations to produce maps detailing the spatial variation of indoor radon concentrations. National surveys which are designed to be representative use either a geographically-weighted or a population-weighted sampling scheme. Additionally, many countries collect a large number of data on indoor radon concentrations from volunteers who have chosen to have the indoor radon concentration measured in their own dwellings. This work examines the representativeness of volunteer-based samples in radon measurement and explores the effect of potential volunteer bias on radon mapping results. We also investigate the influence that media attention has on volunteer sampling of indoor radon concentrations. The result of our work indicates that volunteer measurements are biased due to over-sampling of high radon areas. Consequently such volunteer radon measurements should not be used for radon mapping purposes.

  4. Big data and large sample size: a cautionary note on the potential for bias.

    PubMed

    Kaplan, Robert M; Chambers, David A; Glasgow, Russell E

    2014-08-01

    A number of commentaries have suggested that large studies are more reliable than smaller studies and there is a growing interest in the analysis of "big data" that integrates information from many thousands of persons and/or different data sources. We consider a variety of biases that are likely in the era of big data, including sampling error, measurement error, multiple comparisons errors, aggregation error, and errors associated with the systematic exclusion of information. Using examples from epidemiology, health services research, studies on determinants of health, and clinical trials, we conclude that it is necessary to exercise greater caution to be sure that big sample size does not lead to big inferential errors. Despite the advantages of big studies, large sample size can magnify the bias associated with error resulting from sampling or study design.

  5. Turning intractable counting into sampling: Computing the configurational entropy of three-dimensional jammed packings

    NASA Astrophysics Data System (ADS)

    Martiniani, Stefano; Schrenk, K. Julian; Stevenson, Jacob D.; Wales, David J.; Frenkel, Daan

    2016-01-01

    We present a numerical calculation of the total number of disordered jammed configurations Ω of N repulsive, three-dimensional spheres in a fixed volume V . To make these calculations tractable, we increase the computational efficiency of the approach of Xu et al. [Phys. Rev. Lett. 106, 245502 (2011), 10.1103/PhysRevLett.106.245502] and Asenjo et al. [Phys. Rev. Lett. 112, 098002 (2014), 10.1103/PhysRevLett.112.098002] and we extend the method to allow computation of the configurational entropy as a function of pressure. The approach that we use computes the configurational entropy by sampling the absolute volume of basins of attraction of the stable packings in the potential energy landscape. We find a surprisingly strong correlation between the pressure of a configuration and the volume of its basin of attraction in the potential energy landscape. This relation is well described by a power law. Our methodology to compute the number of minima in the potential energy landscape should be applicable to a wide range of other enumeration problems in statistical physics, string theory, cosmology, and machine learning that aim to find the distribution of the extrema of a scalar cost function that depends on many degrees of freedom.

  6. Turning intractable counting into sampling: Computing the configurational entropy of three-dimensional jammed packings.

    PubMed

    Martiniani, Stefano; Schrenk, K Julian; Stevenson, Jacob D; Wales, David J; Frenkel, Daan

    2016-01-01

    We present a numerical calculation of the total number of disordered jammed configurations Ω of N repulsive, three-dimensional spheres in a fixed volume V. To make these calculations tractable, we increase the computational efficiency of the approach of Xu et al. [Phys. Rev. Lett. 106, 245502 (2011)10.1103/PhysRevLett.106.245502] and Asenjo et al. [Phys. Rev. Lett. 112, 098002 (2014)10.1103/PhysRevLett.112.098002] and we extend the method to allow computation of the configurational entropy as a function of pressure. The approach that we use computes the configurational entropy by sampling the absolute volume of basins of attraction of the stable packings in the potential energy landscape. We find a surprisingly strong correlation between the pressure of a configuration and the volume of its basin of attraction in the potential energy landscape. This relation is well described by a power law. Our methodology to compute the number of minima in the potential energy landscape should be applicable to a wide range of other enumeration problems in statistical physics, string theory, cosmology, and machine learning that aim to find the distribution of the extrema of a scalar cost function that depends on many degrees of freedom.

  7. Bias and imprecision in posture percentile variables estimated from short exposure samples

    PubMed Central

    2012-01-01

    Background Upper arm postures are believed to be an important risk determinant for musculoskeletal disorder development in the neck and shoulders. The 10th and 90th percentiles of the angular elevation distribution have been reported in many studies as measures of neutral and extreme postural exposures, and variation has been quantified by the 10th-90th percentile range. Further, the 50th percentile is commonly reported as a measure of "average" exposure. These four variables have been estimated using samples of observed or directly measured postures, typically using sampling durations between 5 and 120 min. Methods The present study examined the statistical properties of estimated full-shift values of the 10th, 50th and 90th percentile and the 10th-90th percentile range of right upper arm elevation obtained from samples of seven different durations, ranging from 5 to 240 min. The sampling strategies were realized by simulation, using a parent data set of 73 full-shift, continuous inclinometer recordings among hairdressers. For each shift, sampling duration and exposure variable, the mean, standard deviation and sample dispersion limits (2.5% and 97.5%) of all possible sample estimates obtained at one minute intervals were calculated and compared to the true full-shift exposure value. Results Estimates of the 10th percentile proved to be upward biased with limited sampling, and those of the 90th percentile and the percentile range, downward biased. The 50th percentile was also slightly upwards biased. For all variables, bias was more severe with shorter sampling durations, and it correlated significantly with the true full-shift value for the 10th and 90th percentiles and the percentile range. As expected, shorter samples led to decreased precision of the estimate; sample standard deviations correlated strongly with true full-shift exposure values. Conclusions The documented risk of pronounced bias and low precision of percentile estimates obtained from short

  8. Assessing Sample Bias among Venue-Based Respondents at Medical Marijuana Dispensaries.

    PubMed

    Thomas, Crystal; Freisthler, Bridget

    2016-01-01

    Venue-based sampling is the identification of, and outreach to, locations visited by the population of interest for the purpose of collecting data. The method is frequently used to reach specific populations, commonly referred to as "hidden populations." Medical marijuana users represent a hidden population of persons who use marijuana for medicinal purposes. We examine whether venue-based procedures introduce selection or non-respondent bias into the study. The venue based sampling procedures employed for the UCLA Medical Marijuana Study used a two-stage, venue-based sampling approach. First, analyses were conducted to assess potential bias within dispensaries that agreed to participate in the surveys. Secondly, analyses were conducted to examine differences among patrons who responded to surveys. Overall, selection bias was generally absent among study results. Results also illuminated the minimal respondent bias observed among the survey respondents. Results suggest that the use of dispensaries to access and survey medical marijuana users is a viable option to gather patient information that adequately represents the greater population of medical marijuana users in Los Angeles. Thus, recommendations and conclusions based on findings from venue-based studies of medical marijuana users at dispensary sites serve to impartially inform meaningful research.

  9. Assessing Sample Bias among Venue-Based Respondents at Medical Marijuana Dispensaries

    PubMed Central

    Thomas, Crystal; Freisthler, Bridget

    2016-01-01

    Venue-based sampling is the identification of, and outreach to, locations visited by the population of interest for the purpose of collecting data. The method is frequently used to reach specific populations, commonly referred to as “hidden populations.” Medical marijuana users represent a hidden population of persons who use marijuana for medicinal purposes. We examine whether venue-based procedures introduce selection or non-respondent bias into the study. The venue based sampling procedures employed for the UCLA Medical Marijuana Study used a two-stage, venue-based sampling approach. First, analyses were conducted to assess potential bias within dispensaries that agreed to participate in the surveys. Secondly, analyses were conducted to examine differences among patrons who responded to surveys. Overall, selection bias was generally absent among study results. Results also illuminated the minimal respondent bias observed among the survey respondents. Results suggest that the use of dispensaries to access and survey medical marijuana users is a viable option to gather patient information that adequately represents the greater population of medical marijuana users in Los Angeles. Thus, recommendations and conclusions based on findings from venue-based studies of medical marijuana users at dispensary sites serve to impartially inform meaningful research. PMID:26882461

  10. Biases of CO2 Storage in Eddy Flux Measurements pertinent to Vertical Configurations of a Profile System and CO2 Density Averaging

    SciTech Connect

    Yang, Bai; Hanson, Paul J; Riggs, Jeffery S; Pallardy, Stephen G.; Hosman, K. P.; Meyers, T. P.; Wullschleger, Stan D; Gu, Lianhong; Heuer, Mark

    2007-01-01

    CO2 storage in a 30-minute period in a tall forest canopy often makes significant contributions to net ecosystem exchange (NEE) in the early morning and at night. When CO2 storage is properly measured and taken into account, underestimations of NEE on calm nights can be greatly reduced. Using CO2 data from a 12-level profile, we demonstrate that the lower canopy layer (below the thermal inversion) is a disproportional contributor to the total CO2 storage. This is because time derivative of CO2 density ( c/ t) generally shows increasing magnitude of mean and standard deviation with decreasing heights at night and from sunrise to 1000 hr in both growing and dormant seasons. Effects of resolution and configuration in a profiling system on the accuracy of CO2 storage estimation are evaluated by comparing subset profiles to the 12-level benchmark profile. It is demonstrated that the effectiveness of a profiling system in estimating CO2 storage is not only determined by its number of sampling levels but, more importantly, by its vertical configuration. To optimize a profile, one needs to balance the influence of two factors, c/ t and layer thickness, among all vertical sections within a forest. As a key contributor to the total CO2 storage, the lower canopy (with relatively large means and standard deviations of c/ t) requires a higher resolution in a profile system than the layers above. However, if the upper canopy is over-sparsely sampled relative to the lower canopy, the performance of a profile system might be degraded since, in such a situation, the influence of layer thickness dominates over that of c/ t. We also find that, because of different level of complexity in canopy structure, more sampling levels are necessary at our site in order to achieve the same level of accuracy as at a boreal aspen site. These results suggest that, in order to achieve an adequate accuracy in CO2 storage measurements, the number of sampling levels in a profile and its design should

  11. The importance of measuring and accounting for potential biases in respondent-driven samples.

    PubMed

    Rudolph, Abby E; Fuller, Crystal M; Latkin, Carl

    2013-07-01

    Respondent-driven sampling (RDS) is often viewed as a superior method for recruiting hard-to-reach populations disproportionately burdened with poor health outcomes. As an analytic approach, it has been praised for its ability to generate unbiased population estimates via post-stratified weights which account for non-random recruitment. However, population estimates generated with RDSAT (RDS Analysis Tool) are sensitive to variations in degree weights. Several assumptions are implicit in the degree weight and are not routinely assessed. Failure to meet these assumptions could result in inaccurate degree measures and consequently result in biased population estimates. We highlight potential biases associated with violating the assumptions implicit in degree weights for the RDSAT estimator and propose strategies to measure and possibly correct for biases in the analysis.

  12. The importance of measuring and accounting for potential biases in respondent-driven samples

    PubMed Central

    Rudolph, Abby E.; Fuller, Crystal M.; Latkin, Carl

    2013-01-01

    Respondent-driven sampling (RDS) is often viewed as a superior method for recruiting hard-to-reach populations disproportionately burdened with poor health outcomes. As an analytic approach, it has been praised for its ability to generate unbiased population estimates via post-stratified weights which account for non-random recruitment. However, population estimates generated with RDSAT (RDS Analysis Tool) are sensitive to variations in degree weights. Several assumptions are implicit in the degree weight and are not routinely assessed. Failure to meet these assumptions could result in inaccurate degree measures and consequently result in biased population estimates. We highlight potential biases associated with violating the assumptions implicit in degree weights for the RDSAT estimator and propose strategies to measure and possibly correct for biases in the analysis. PMID:23515641

  13. Origin of tensile strength of a woven sample cut in bias directions

    PubMed Central

    Pan, Ning; Kovar, Radko; Dolatabadi, Mehdi Kamali; Wang, Ping; Zhang, Diantang; Sun, Ying; Chen, Li

    2015-01-01

    Textile fabrics are highly anisotropic, so that their mechanical properties including strengths are a function of direction. An extreme case is when a woven fabric sample is cut in such a way where the bias angle and hence the tension loading direction is around 45° relative to the principal directions. Then, once loaded, no yarn in the sample is held at both ends, so the yarns have to build up their internal tension entirely via yarn–yarn friction at the interlacing points. The overall fabric strength in such a sample is a result of contributions from the yarns being pulled out and those broken during the process, and thus becomes a function of the bias direction angle θ, sample width W and length L, along with other factors known to affect fabric strength tested in principal directions. Furthermore, in such a bias sample when the major parameters, e.g. the sample width W, change, not only the resultant strengths differ, but also the strength generating mechanisms (or failure types) vary. This is an interesting problem and is analysed in this study. More specifically, the issues examined in this paper include the exact mechanisms and details of how each interlacing point imparts the frictional constraint for a yarn to acquire tension to the level of its strength when both yarn ends were not actively held by the testing grips; the theoretical expression of the critical yarn length for a yarn to be able to break rather than be pulled out, as a function of the related factors; and the general relations between the tensile strength of such a bias sample and its structural properties. At the end, theoretical predictions are compared with our experimental data. PMID:26064655

  14. Monitoring the aftermath of Flint drinking water contamination crisis: Another case of sampling bias?

    PubMed

    Goovaerts, Pierre

    2017-07-15

    The delay in reporting high levels of lead in Flint drinking water, following the city's switch to the Flint River as its water supply, was partially caused by the biased selection of sampling sites away from the lead pipe network. Since Flint returned to its pre-crisis source of drinking water, the State has been monitoring water lead levels (WLL) at selected "sentinel" sites. In a first phase that lasted two months, 739 residences were sampled, most of them bi-weekly, to determine the general health of the distribution system and to track temporal changes in lead levels. During the same period, water samples were also collected through a voluntary program whereby concerned citizens received free testing kits and conducted sampling on their own. State officials relied on the former data to demonstrate the steady improvement in water quality. A recent analysis of data collected by voluntary sampling revealed, however, an opposite trend with lead levels increasing over time. This paper looks at potential sampling bias to explain such differences. Although houses with higher WLL were more likely to be sampled repeatedly, voluntary sampling turned out to reproduce fairly well the main characteristics (i.e. presence of lead service lines (LSL), construction year) of Flint housing stock. State-controlled sampling was less representative; e.g., sentinel sites with LSL were mostly built between 1935 and 1950 in lower poverty areas, which might hamper our ability to disentangle the effects of LSL and premise plumbing (lead fixtures and pipes present within old houses) on WLL. Also, there was no sentinel site with LSL in two of the most impoverished wards, including where the percentage of children with elevated blood lead levels tripled following the switch in water supply. Correcting for sampling bias narrowed the gap between sampling programs, yet overall temporal trends are still opposite.

  15. Symmetry and random sampling of symmetry independent configurations for the simulation of disordered solids.

    PubMed

    D'Arco, Philippe; Mustapha, Sami; Ferrabone, Matteo; Noël, Yves; De La Pierre, Marco; Dovesi, Roberto

    2013-09-04

    A symmetry-adapted algorithm producing uniformly at random the set of symmetry independent configurations (SICs) in disordered crystalline systems or solid solutions is presented here. Starting from Pólya's formula, the role of the conjugacy classes of the symmetry group in uniform random sampling is shown. SICs can be obtained for all the possible compositions or for a chosen one, and symmetry constraints can be applied. The approach yields the multiplicity of the SICs and allows us to operate configurational statistics in the reduced space of the SICs. The present low-memory demanding implementation is briefly sketched. The probability of finding a given SIC or a subset of SICs is discussed as a function of the number of draws and their precise estimate is given. The method is illustrated by application to a binary series of carbonates and to the binary spinel solid solution Mg(Al,Fe)2O4.

  16. Personality, Attentional Biases towards Emotional Faces and Symptoms of Mental Disorders in an Adolescent Sample.

    PubMed

    O'Leary-Barrett, Maeve; Pihl, Robert O; Artiges, Eric; Banaschewski, Tobias; Bokde, Arun L W; Büchel, Christian; Flor, Herta; Frouin, Vincent; Garavan, Hugh; Heinz, Andreas; Ittermann, Bernd; Mann, Karl; Paillère-Martinot, Marie-Laure; Nees, Frauke; Paus, Tomas; Pausova, Zdenka; Poustka, Luise; Rietschel, Marcella; Robbins, Trevor W; Smolka, Michael N; Ströhle, Andreas; Schumann, Gunter; Conrod, Patricia J

    2015-01-01

    To investigate the role of personality factors and attentional biases towards emotional faces, in establishing concurrent and prospective risk for mental disorder diagnosis in adolescence. Data were obtained as part of the IMAGEN study, conducted across 8 European sites, with a community sample of 2257 adolescents. At 14 years, participants completed an emotional variant of the dot-probe task, as well two personality measures, namely the Substance Use Risk Profile Scale and the revised NEO Personality Inventory. At 14 and 16 years, participants and their parents were interviewed to determine symptoms of mental disorders. Personality traits were general and specific risk indicators for mental disorders at 14 years. Increased specificity was obtained when investigating the likelihood of mental disorders over a 2-year period, with the Substance Use Risk Profile Scale showing incremental validity over the NEO Personality Inventory. Attentional biases to emotional faces did not characterise or predict mental disorders examined in the current sample. Personality traits can indicate concurrent and prospective risk for mental disorders in a community youth sample, and identify at-risk youth beyond the impact of baseline symptoms. This study does not support the hypothesis that attentional biases mediate the relationship between personality and psychopathology in a community sample. Task and sample characteristics that contribute to differing results among studies are discussed.

  17. Personality, Attentional Biases towards Emotional Faces and Symptoms of Mental Disorders in an Adolescent Sample

    PubMed Central

    O’Leary-Barrett, Maeve; Pihl, Robert O.; Artiges, Eric; Banaschewski, Tobias; Bokde, Arun L. W.; Büchel, Christian; Flor, Herta; Frouin, Vincent; Garavan, Hugh; Heinz, Andreas; Ittermann, Bernd; Mann, Karl; Paillère-Martinot, Marie-Laure; Nees, Frauke; Paus, Tomas; Pausova, Zdenka; Poustka, Luise; Rietschel, Marcella; Robbins, Trevor W.; Smolka, Michael N.; Ströhle, Andreas; Schumann, Gunter; Conrod, Patricia J.

    2015-01-01

    Objective To investigate the role of personality factors and attentional biases towards emotional faces, in establishing concurrent and prospective risk for mental disorder diagnosis in adolescence. Method Data were obtained as part of the IMAGEN study, conducted across 8 European sites, with a community sample of 2257 adolescents. At 14 years, participants completed an emotional variant of the dot-probe task, as well two personality measures, namely the Substance Use Risk Profile Scale and the revised NEO Personality Inventory. At 14 and 16 years, participants and their parents were interviewed to determine symptoms of mental disorders. Results Personality traits were general and specific risk indicators for mental disorders at 14 years. Increased specificity was obtained when investigating the likelihood of mental disorders over a 2-year period, with the Substance Use Risk Profile Scale showing incremental validity over the NEO Personality Inventory. Attentional biases to emotional faces did not characterise or predict mental disorders examined in the current sample. Discussion Personality traits can indicate concurrent and prospective risk for mental disorders in a community youth sample, and identify at-risk youth beyond the impact of baseline symptoms. This study does not support the hypothesis that attentional biases mediate the relationship between personality and psychopathology in a community sample. Task and sample characteristics that contribute to differing results among studies are discussed. PMID:26046352

  18. The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography.

    PubMed

    Lapierre, Marguerite; Blin, Camille; Lambert, Amaury; Achaz, Guillaume; Rocha, Eduardo P C

    2016-07-01

    Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombination (gene conversion), and sampling biases on demographic inference using skyline plots and site frequency spectra (SFS). Forward simulations based on biologically relevant parameters from Escherichia coli populations showed that theoretical arguments on the detrimental impact of recombination and especially natural selection on the reconstructed genealogies cannot be ignored in practice. In fact, both processes systematically lead to spurious interpretations of population expansion in skyline plots (and in SFS for selection). Weak purifying selection, and especially positive selection, had important effects on skyline plots, showing patterns akin to those of population expansions. State-of-the-art techniques to remove recombination further amplified these biases. We simulated three common sampling biases in microbiological research: uniform, clustered, and mixed sampling. Alone, or together with recombination and selection, they further mislead demographic inferences producing almost any possible skyline shape or SFS. Interestingly, sampling sub-populations also affected skyline plots and SFS, because the coalescent rates of populations and their sub-populations had different distributions. This study suggests that extreme caution is needed to infer demographic changes solely based on reconstructed genealogies. We suggest that the development of novel sampling strategies and the joint analyzes of diverse population genetic methods are strictly necessary to estimate demographic changes in populations where selection, recombination, and biased sampling are present. © The Author 2016. Published by Oxford University Press on behalf of the Society for

  19. The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography

    PubMed Central

    Lapierre, Marguerite; Blin, Camille; Lambert, Amaury; Achaz, Guillaume; Rocha, Eduardo P. C.

    2016-01-01

    Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombination (gene conversion), and sampling biases on demographic inference using skyline plots and site frequency spectra (SFS). Forward simulations based on biologically relevant parameters from Escherichia coli populations showed that theoretical arguments on the detrimental impact of recombination and especially natural selection on the reconstructed genealogies cannot be ignored in practice. In fact, both processes systematically lead to spurious interpretations of population expansion in skyline plots (and in SFS for selection). Weak purifying selection, and especially positive selection, had important effects on skyline plots, showing patterns akin to those of population expansions. State-of-the-art techniques to remove recombination further amplified these biases. We simulated three common sampling biases in microbiological research: uniform, clustered, and mixed sampling. Alone, or together with recombination and selection, they further mislead demographic inferences producing almost any possible skyline shape or SFS. Interestingly, sampling sub-populations also affected skyline plots and SFS, because the coalescent rates of populations and their sub-populations had different distributions. This study suggests that extreme caution is needed to infer demographic changes solely based on reconstructed genealogies. We suggest that the development of novel sampling strategies and the joint analyzes of diverse population genetic methods are strictly necessary to estimate demographic changes in populations where selection, recombination, and biased sampling are present. PMID:26931140

  20. Bias in C IV-based quasar black hole mass scaling relationships from reverberation mapped samples

    NASA Astrophysics Data System (ADS)

    Brotherton, Michael S.; Runnoe, J. C.; Shang, Zhaohui; DiPompeo, M. A.

    2015-08-01

    The masses of the black holes powering quasars represent a fundamental parameter of active galaxies. Estimates of quasar black hole masses using single-epoch spectra are quite uncertain, and require quantitative improvement. We recently identified a correction for C IV λ1549-based scaling relationships used to estimate quasar black hole masses that relies on the continuum-subtracted peak flux ratio of the ultraviolet emission-line blend Si IV + O IV] (the λ1400 feature) to that of C IV. This parameter correlates with the suite of associated quasar spectral properties collectively known as `Eigenvector 1' (EV1). Here we use a sample of 85 quasars with quasi-simultaneous optical-ultraviolet spectrophotometry to demonstrate how biases in the average EV1 properties can create systematic biases in C IV-based black hole mass scaling relationships. This effect results in nearly an order of magnitude moving from objects with small , which have overestimated black hole masses, to objects with large , which have underestimated values. We show that existing reverberation-mapped samples of quasars with ultraviolet spectra - used to calibrate C IV-based scaling relationships - have significant EV1 biases that result in predictions of black hole masses nearly 50 per cent too high for the average quasar. We offer corrections and suggestions to account for this bias.

  1. Estimating sampling biases and measurement uncertainties of AIRS/AMSU-A temperature and water vapor observations using MERRA reanalysis

    NASA Astrophysics Data System (ADS)

    Hearty, Thomas J.; Savtchenko, Andrey; Tian, Baijun; Fetzer, Eric; Yung, Yuk L.; Theobald, Michael; Vollmer, Bruce; Fishbein, Evan; Won, Young-In

    2014-03-01

    We use MERRA (Modern Era Retrospective-Analysis for Research Applications) temperature and water vapor data to estimate the sampling biases of climatologies derived from the AIRS/AMSU-A (Atmospheric Infrared Sounder/Advanced Microwave Sounding Unit-A) suite of instruments. We separate the total sampling bias into temporal and instrumental components. The temporal component is caused by the AIRS/AMSU-A orbit and swath that are not able to sample all of time and space. The instrumental component is caused by scenes that prevent successful retrievals. The temporal sampling biases are generally smaller than the instrumental sampling biases except in regions with large diurnal variations, such as the boundary layer, where the temporal sampling biases of temperature can be ± 2 K and water vapor can be 10% wet. The instrumental sampling biases are the main contributor to the total sampling biases and are mainly caused by clouds. They are up to 2 K cold and > 30% dry over midlatitude storm tracks and tropical deep convective cloudy regions and up to 20% wet over stratus regions. However, other factors such as surface emissivity and temperature can also influence the instrumental sampling bias over deserts where the biases can be up to 1 K cold and 10% wet. Some instrumental sampling biases can vary seasonally and/or diurnally. We also estimate the combined measurement uncertainties of temperature and water vapor from AIRS/AMSU-A and MERRA by comparing similarly sampled climatologies from both data sets. The measurement differences are often larger than the sampling biases and have longitudinal variations.

  2. Estimating Sampling Biases and Measurement Uncertainties of AIRS-AMSU-A Temperature and Water Vapor Observations Using MERRA Reanalysis

    NASA Technical Reports Server (NTRS)

    Hearty, Thomas J.; Savtchenko, Andrey K.; Tian, Baijun; Fetzer, Eric; Yung, Yuk L.; Theobald, Michael; Vollmer, Bruce; Fishbein, Evan; Won, Young-In

    2014-01-01

    We use MERRA (Modern Era Retrospective-Analysis for Research Applications) temperature and water vapor data to estimate the sampling biases of climatologies derived from the AIRS/AMSU-A (Atmospheric Infrared Sounder/Advanced Microwave Sounding Unit-A) suite of instruments. We separate the total sampling bias into temporal and instrumental components. The temporal component is caused by the AIRS/AMSU-A orbit and swath that are not able to sample all of time and space. The instrumental component is caused by scenes that prevent successful retrievals. The temporal sampling biases are generally smaller than the instrumental sampling biases except in regions with large diurnal variations, such as the boundary layer, where the temporal sampling biases of temperature can be +/- 2 K and water vapor can be 10% wet. The instrumental sampling biases are the main contributor to the total sampling biases and are mainly caused by clouds. They are up to 2 K cold and greater than 30% dry over mid-latitude storm tracks and tropical deep convective cloudy regions and up to 20% wet over stratus regions. However, other factors such as surface emissivity and temperature can also influence the instrumental sampling bias over deserts where the biases can be up to 1 K cold and 10% wet. Some instrumental sampling biases can vary seasonally and/or diurnally. We also estimate the combined measurement uncertainties of temperature and water vapor from AIRS/AMSU-A and MERRA by comparing similarly sampled climatologies from both data sets. The measurement differences are often larger than the sampling biases and have longitudinal variations.

  3. A large sample of binary quasars: Does quasar bias tracks from Mpc scale to kpc scales?

    NASA Astrophysics Data System (ADS)

    Eftekharzadeh, Sarah; Myers, Adam D.; Djorgovski, Stanislav G.; Graham, Matthew J.

    2017-01-01

    We present the most precise estimate to date of the bias of quasars on very small scales, based on a measurement of the clustering of 47 spectroscopically confirmed binary quasars with proper transverse separations of ~25 h^{-1} kpc. The quasars in our sample, which is an order-of-magnitude larger than previous samples, are targeted using a Kernel Density Estimation technique (KDE) applied to Sloan Digital Sky Survey (SDSS) imaging over most of the SDSS area. Our sample is "complete," in that all possible pairs of binary quasars across our area of interest have been spectroscopically confirmed from a combination of previous surveys and our own long-slit observational campaign. We determine the projected correlation function of quasars (\\bar W_p) in four bins of proper transverse scale over the range 17.0 \\lesssim R_{prop} \\lesssim 36.2 h^{-1} kpc. Due to our large sample size, our measured projected correlation function in each of these four bins of scale is more than twice as precise as any previous measurement made over our {\\em full} range of scales. We also measure the bias of our quasar sample in four slices of redshift across the range 0.43 \\le z \\le 2.26 and compare our results to similar measurements of how quasar bias evolves on Mpc-scales. This measurement addresses the question of whether it is reasonable to assume that quasar bias evolves with redshift in a similar fashion on both Mpc and kpc scales. Our results can meaningfully constrain the one-halo term of the Halo Occupation Distribution (HOD) of quasars and how it evolves with redshift. This work was partially supported by NSF grant 1515404.

  4. Anticipation or ascertainment bias in schizophrenia? Penrose`s familial mental illness sample

    SciTech Connect

    Bassett, A.S. |; Husted, J.

    1997-03-01

    Several studies have observed anticipation (earlier age at onset [AAO] in successive generations) in familial schizophrenia. However, whether true anticipation or ascertainment bias is the principal originating mechanism remains unclear. In 1944 L.S. Penrose collected AAO data on a large, representative sample of familial mental illness, using a broad ascertainment strategy. These data allowed examination of anticipation and ascertainment biases in five two-generation samples of affected relative pairs. The median intergenerational difference (MID) in AAO was used to assess anticipation. Results showed significant anticipation in parent-offspring pairs with schizophrenia (n = 137 pairs; MID 15 years; P = .0001) and in a positive control sample with Huntington disease (n = 11; P = .01). Broadening the diagnosis of the schizophrenia sample suggested anticipation of severity of illness. However, other analyses provided evidence for ascertainment bias, especially in later-AAO parents, in parent-offspring pairs. Aunt/uncle-niece/nephew schizophrenia pairs showed anticipation (n = 111; P = .0001), but the MID was 8 years and aunts/uncles had earlier median AAO than parents. Anticipation effects were greatest in pairs with late-AAO parents but remained significant in a subgroup of schizophrenia pairs with early parental AAO (n = 31; P = .03). A small control sample of other diseases had MID of 5 years but no significant anticipation (n = 9; F = .38). These results suggest that, although ascertainment-bias effects were observed in parent-offspring pairs, true anticipation appears to be inherent in the transmission of familial schizophrenia. The findings support investigations of unstable mutations and other mechanisms that may contribute to true anticipation in schizophrenia. 37 refs., 2 tabs.

  5. Anticipating species distributions: Handling sampling effort bias under a Bayesian framework.

    PubMed

    Rocchini, Duccio; Garzon-Lopez, Carol X; Marcantonio, Matteo; Amici, Valerio; Bacaro, Giovanni; Bastin, Lucy; Brummitt, Neil; Chiarucci, Alessandro; Foody, Giles M; Hauffe, Heidi C; He, Kate S; Ricotta, Carlo; Rizzoli, Annapaola; Rosà, Roberto

    2017-04-15

    Anticipating species distributions in space and time is necessary for effective biodiversity conservation and for prioritising management interventions. This is especially true when considering invasive species. In such a case, anticipating their spread is important to effectively plan management actions. However, considering uncertainty in the output of species distribution models is critical for correctly interpreting results and avoiding inappropriate decision-making. In particular, when dealing with species inventories, the bias resulting from sampling effort may lead to an over- or under-estimation of the local density of occurrences of a species. In this paper we propose an innovative method to i) map sampling effort bias using cartogram models and ii) explicitly consider such uncertainty in the modeling procedure under a Bayesian framework, which allows the integration of multilevel input data with prior information to improve the anticipation species distributions.

  6. Correction of sampling bias in a cross-sectional study of post-surgical complications.

    PubMed

    Fluss, Ronen; Mandel, Micha; Freedman, Laurence S; Weiss, Inbal Salz; Zohar, Anat Ekka; Haklai, Ziona; Gordon, Ethel-Sherry; Simchen, Elisheva

    2013-06-30

    Cross-sectional designs are often used to monitor the proportion of infections and other post-surgical complications acquired in hospitals. However, conventional methods for estimating incidence proportions when applied to cross-sectional data may provide estimators that are highly biased, as cross-sectional designs tend to include a high proportion of patients with prolonged hospitalization. One common solution is to use sampling weights in the analysis, which adjust for the sampling bias inherent in a cross-sectional design. The current paper describes in detail a method to build weights for a national survey of post-surgical complications conducted in Israel. We use the weights to estimate the probability of surgical site infections following colon resection, and validate the results of the weighted analysis by comparing them with those obtained from a parallel study with a historically prospective design. Copyright © 2012 John Wiley & Sons, Ltd.

  7. Tunable WDM sampling pulse streams using a spatial phase modulator in a biased pulse shaper.

    PubMed

    Sinefeld, David; Shayovitz, Dror; Golani, Ori; Marom, Dan M

    2014-02-01

    We generate transform-limited WDM optical sampling pulse bursts by filtering ultrashort pulses from a mode-locked laser. A phase spatial light modulator (SLM) is used in a biased pulse shaper to circumvent the need to modulate with 2π phase wraps, which are known to limit the phase response. The arrangement compresses and retimes user-selectable bandwidths from the optical short pulse source with precise control of pulse bandwidth, pulse stream rates, and duty cycle.

  8. Sample-Size Planning for More Accurate Statistical Power: A Method Adjusting Sample Effect Sizes for Publication Bias and Uncertainty.

    PubMed

    Anderson, Samantha F; Kelley, Ken; Maxwell, Scott E

    2017-09-01

    The sample size necessary to obtain a desired level of statistical power depends in part on the population value of the effect size, which is, by definition, unknown. A common approach to sample-size planning uses the sample effect size from a prior study as an estimate of the population value of the effect to be detected in the future study. Although this strategy is intuitively appealing, effect-size estimates, taken at face value, are typically not accurate estimates of the population effect size because of publication bias and uncertainty. We show that the use of this approach often results in underpowered studies, sometimes to an alarming degree. We present an alternative approach that adjusts sample effect sizes for bias and uncertainty, and we demonstrate its effectiveness for several experimental designs. Furthermore, we discuss an open-source R package, BUCSS, and user-friendly Web applications that we have made available to researchers so that they can easily implement our suggested methods.

  9. Potential bias of daily soil CO2 efflux estimates due to sampling time.

    PubMed

    Cueva, Alejandro; Bullock, Stephen H; López-Reyes, Eulogio; Vargas, Rodrigo

    2017-09-20

    Soil respiration (Rs) has been usually measured during daylight hours using manual chambers. This approach assumes that measurements made during a typical time interval (e.g., 9 to 11 am) represent the mean daily value; locally, this may not always be correct and could result in systematic bias of daily and annual Rs budgets. We propose a simple method, based on the temporal stability concept, to determine the most appropriate time of the day for manual measurements to capture a representative mean daily Rs value. We introduce a correction factor to adjust for biases due to non-optimally timed sampling. This approach was tested in a semiarid shrubland using 24 hr campaigns using two treatments: trenched plots and plots with shrubs. In general, we found optimum times were at night and potential biases ranged from -29 to + 40% in relation to the 24 hr mean of Rs, especially in trenched plots. The degree of bias varied between treatments and seasons, having a greater influence during the wet season when efflux was high than during the dry season when efflux was low. This study proposes a framework for improving local Rs estimates that informs how to decrease temporal uncertainties in upscaling to the annual total.

  10. Studies on natural recovery from alcohol dependence: sample selection bias by media solicitation?

    PubMed

    Rumpf, H J; Bischof, G; Hapke, U; Meyer, C; John, U

    2000-05-01

    To assess the selection bias of recruiting participants in studies on natural recovery from alcohol dependence through media solicitation. Two samples with different recruitment strategies are compared. Media solicitation and general population. Sample 1 consists of 176 alcohol-dependent individuals remitted without formal help and recruited through media solicitation, sample 2 consists of 32 natural remitters derived from a representative general population study with a sample size of 4075 respondents and a response rate of 70.2%. Several triggering mechanisms and maintenance factors of remission were assessed in a personal interview using standardized questionnaires. Results of logistic regression analyses show that media-solicited subjects were more often abstinent in the last 12 months, were more severely dependent, were less satisfied with eight life domains prior to remission and showed higher scores in a coping behaviour measure. Besides these major differences from the multivariate analysis, media subjects revealed more health problems prior to remission, experienced more social pressure to change drinking behaviour, and showed differences in reasons for not seeking help. Media solicitation leads to a sample selection bias in research on natural recovery from alcohol dependence. When measures to foster self-change are derived from such studies, findings from representative samples have to be considered.

  11. Reliable measurements for an image-derived sample volume in an open-configuration MR system

    NASA Astrophysics Data System (ADS)

    Han, Bong Soo; Lee, Man Woo; Hong, Cheolpyo

    2016-11-01

    Open-configuration magnetic resonance (MR) systems are becoming desirable for volume measurements of off-center samples due to their non-claustrophobic system configuration, excellent soft-tissue contrast, high efficiency, and low-cost. However, geometric distortion is produced by the unwanted background magnetic field and hinders volume measurements. The present study describes the characteristics of geometric distortion in off-center samples such as the thigh muscle and adipose tissue measurements using an open-type MR system. The American Association of Physicists in Medicine uniformity and linearity phantom was used for the detection and the evaluation of the geometric distortion. The geometric distortion decreased near the isocenter and increased toward the off-center. A cylindrical phantom image was acquired at the isocenter and was used as the distortion-free, reference image. Two cylindrical phantoms were scanned off-center at a position analogous to that of the human thigh. The differences between the two cylindrical phantom volumes and the reference volume were 1.62 % ± 0.16 and 5.18 % ± 0.14. Off-center-related MR imaging requires careful consideration for image interpretation and volumetric assessment of tissue.

  12. Displaying bias in sampling effort of data accessed from biodiversity databases using ignorance maps.

    PubMed

    Ruete, Alejandro

    2015-01-01

    Open-access biodiversity databases including mainly citizen science data make temporally and spatially extensive species' observation data available to a wide range of users. Such data have limitations however, which include: sampling bias in favour of recorder distribution, lack of survey effort assessment, and lack of coverage of the distribution of all organisms. These limitations are not always recorded, while any technical assessment or scientific research based on such data should include an evaluation of the uncertainty of its source data and researchers should acknowledge this information in their analysis. The here proposed maps of ignorance are a critical and easy way to implement a tool to not only visually explore the quality of the data, but also to filter out unreliable results. I present simple algorithms to display ignorance maps as a tool to report the spatial distribution of the bias and lack of sampling effort across a study region. Ignorance scores are expressed solely based on raw data in order to rely on the fewest assumptions possible. Therefore there is no prediction or estimation involved. The rationale is based on the assumption that it is appropriate to use species groups as a surrogate for sampling effort because it is likely that an entire group of species observed by similar methods will share similar bias. Simple algorithms are then used to transform raw data into ignorance scores scaled 0-1 that are easily comparable and scalable. Because of the need to perform calculations over big datasets, simplicity is crucial for web-based implementations on infrastructures for biodiversity information. With these algorithms, any infrastructure for biodiversity information can offer a quality report of the observations accessed through them. Users can specify a reference taxonomic group and a time frame according to the research question. The potential of this tool lies in the simplicity of its algorithms and in the lack of assumptions made

  13. Periodontal Research: Basics and beyond – Part II (Ethical issues, sampling, outcome measures and bias)

    PubMed Central

    Avula, Haritha

    2013-01-01

    A good research beginning refers to formulating a well-defined research question, developing a hypothesis and choosing an appropriate study design. The first part of the review series has discussed these issues in depth and this paper intends to throw light on other issues pertaining to the implementation of research. These include the various ethical norms and standards in human experimentation, the eligibility criteria for the participants, sampling methods and sample size calculation, various outcome measures that need to be defined and the biases that can be introduced in research. PMID:24174747

  14. Implicit and Explicit Weight Bias in a National Sample of 4732 Medical Students: The Medical Student CHANGES Study

    PubMed Central

    Phelan, Sean M.; Dovidio, John F.; Puhl, Rebecca M.; Burgess, Diana J.; Nelson, David B.; Yeazel, Mark W.; Hardeman, Rachel; Perry, Sylvia; van Ryn, Michelle

    2014-01-01

    Objective To examine the magnitude of explicit and implicit weight biases compared to biases against other groups; and identify student factors predicting bias in a large national sample of medical students. Design and Methods A web-based survey was completed by 4732 1st year medical students from 49 medical schools as part of a longitudinal study of medical education. The survey included a validated measure of implicit weight bias, the implicit association test, and 2 measures of explicit bias: a feeling thermometer and the anti-fat attitudes test. Results A majority of students exhibited implicit (74%) and explicit (67%) weight bias. Implicit weight bias scores were comparable to reported bias against racial minorities. Explicit attitudes were more negative toward obese people than toward racial minorities, gays, lesbians, and poor people. In multivariate regression models, implicit and explicit weight bias was predicted by lower BMI, male sex, and non-Black race. Either implicit or explicit bias was also predicted by age, SES, country of birth, and specialty choice. Conclusions Implicit and explicit weight bias is common among 1st year medical students, and varies across student factors. Future research should assess implications of biases and test interventions to reduce their impact. PMID:24375989

  15. Implicit and explicit weight bias in a national sample of 4,732 medical students: the medical student CHANGES study.

    PubMed

    Phelan, Sean M; Dovidio, John F; Puhl, Rebecca M; Burgess, Diana J; Nelson, David B; Yeazel, Mark W; Hardeman, Rachel; Perry, Sylvia; van Ryn, Michelle

    2014-04-01

    To examine the magnitude of explicit and implicit weight biases compared to biases against other groups; and identify student factors predicting bias in a large national sample of medical students. A web-based survey was completed by 4,732 1st year medical students from 49 medical schools as part of a longitudinal study of medical education. The survey included a validated measure of implicit weight bias, the implicit association test, and 2 measures of explicit bias: a feeling thermometer and the anti-fat attitudes test. A majority of students exhibited implicit (74%) and explicit (67%) weight bias. Implicit weight bias scores were comparable to reported bias against racial minorities. Explicit attitudes were more negative toward obese people than toward racial minorities, gays, lesbians, and poor people. In multivariate regression models, implicit and explicit weight bias was predicted by lower BMI, male sex, and non-Black race. Either implicit or explicit bias was also predicted by age, SES, country of birth, and specialty choice. Implicit and explicit weight bias is common among 1st year medical students, and varies across student factors. Future research should assess implications of biases and test interventions to reduce their impact. Copyright © 2013 The Obesity Society.

  16. Development of a depth-integrated sample arm to reduce solids stratification bias in stormwater sampling

    USGS Publications Warehouse

    Selbig, W.R.; Bannerman, R.T.

    2011-01-01

    A new depth-integrated sample arm (DISA) was developed to improve the representation of solids in stormwater, both organic and inorganic, by collecting a water quality sample from multiple points in the water column. Data from this study demonstrate the idea of vertical stratification of solids in storm sewer runoff. Concentrations of suspended sediment in runoff were statistically greater using a fixed rather than multipoint collection system. Median suspended sediment concentrations measured at the fixed location (near the pipe invert) were approximately double those collected using the DISA. In general, concentrations and size distributions of suspended sediment decreased with increasing vertical distance from the storm sewer invert. Coarser particles tended to dominate the distribution of solids near the storm sewer invert as discharge increased. In contrast to concentration and particle size, organic material, to some extent, was distributed homogenously throughout the water column, likely the result of its low specific density, which allows for thorough mixing in less turbulent water. ?? 2010 Publishing Technology.

  17. Bias in telephone surveys that do not sample cell phones: uses and limits of poststratification adjustments.

    PubMed

    Call, Kathleen Thiede; Davern, Michael; Boudreaux, Michel; Johnson, Pamela Jo; Nelson, Justine

    2011-04-01

    To examine how biased health surveys are when they omit cell phone-only households (CPOH) and to explore whether poststratification can reduce this bias. We used data from the 2008 National Health Interview Survey (NHIS), which uses area probability sampling and in-person interviews; as a result people of all phone statuses are included. First, we examined whether people living in CPOH are different from those not living in CPOH with respect to several important health surveillance domains. We compared standard NHIS estimates to a set of "reweighted" estimates that exclude people living in CPHO. The reweighted NHIS cases were fitted through a series of poststratification adjustments to NHIS control totals. In addition to poststratification adjustments for region, race or ethnicity, and age, we examined adjustments for home ownership, age by education, and household structure. Poststratification reduces bias in all health-related estimates for the nonelderly population. However, these adjustments work less well for Hispanics and blacks and even worse for young adults (18 to 30 y). Reduction in bias is greatest for estimates of uninsurance and having no usual source of care, and worse for estimates of drinking, smoking, and forgone or delayed care because of costs. Applying poststratification adjustments to data that exclude CPOH works well at the total population level for estimates such as health insurance, and less well for access and health behaviors. However, poststratification adjustments do not do enough to reduce bias in health-related estimates at the subpopulation level, particularly for those interested in measuring and monitoring racial, ethnic, and age disparities.

  18. Pathogen prevalence, group bias, and collectivism in the standard cross-cultural sample.

    PubMed

    Cashdan, Elizabeth; Steele, Matthew

    2013-03-01

    It has been argued that people in areas with high pathogen loads will be more likely to avoid outsiders, to be biased in favor of in-groups, and to hold collectivist and conformist values. Cross-national studies have supported these predictions. In this paper we provide new pathogen codes for the 186 cultures of the Standard Cross-Cultural Sample and use them, together with existing pathogen and ethnographic data, to try to replicate these cross-national findings. In support of the theory, we found that cultures in high pathogen areas were more likely to socialize children toward collectivist values (obedience rather than self-reliance). There was some evidence that pathogens were associated with reduced adult dispersal. However, we found no evidence of an association between pathogens and our measures of group bias (in-group loyalty and xenophobia) or intergroup contact.

  19. Improving the efficiency of configurational-bias Monte Carlo: A density-guided method for generating bending angle trials for linear and branched molecules

    SciTech Connect

    Sepehri, Aliasghar; Loeffler, Troy D.; Chen, Bin

    2014-08-21

    A new method has been developed to generate bending angle trials to improve the acceptance rate and the speed of configurational-bias Monte Carlo. Whereas traditionally the trial geometries are generated from a uniform distribution, in this method we attempt to use the exact probability density function so that each geometry generated is likely to be accepted. In actual practice, due to the complexity of this probability density function, a numerical representation of this distribution function would be required. This numerical table can be generated a priori from the distribution function. This method has been tested on a united-atom model of alkanes including propane, 2-methylpropane, and 2,2-dimethylpropane, that are good representatives of both linear and branched molecules. It has been shown from these test cases that reasonable approximations can be made especially for the highly branched molecules to reduce drastically the dimensionality and correspondingly the amount of the tabulated data that is needed to be stored. Despite these approximations, the dependencies between the various geometrical variables can be still well considered, as evident from a nearly perfect acceptance rate achieved. For all cases, the bending angles were shown to be sampled correctly by this method with an acceptance rate of at least 96% for 2,2-dimethylpropane to more than 99% for propane. Since only one trial is required to be generated for each bending angle (instead of thousands of trials required by the conventional algorithm), this method can dramatically reduce the simulation time. The profiling results of our Monte Carlo simulation code show that trial generation, which used to be the most time consuming process, is no longer the time dominating component of the simulation.

  20. Membrane-based sample preparation for ion chromatography-Techniques, instrumental configurations and applications.

    PubMed

    Frenzel, Wolfgang; Markeviciute, Inga

    2017-01-06

    Sample preparation is the bottleneck of many analytical methods, including ion chromatography (IC). Procedures based on the application of membranes are important, yet not well appreciated means for clean-up and analyte preconcentration of liquid samples. Filtration, ultrafiltration, the variety of dialysis techniques, i.e. passive dialysis, Donnan dialysis and electrodialysis, as well as gas-diffusion are being reviewed here with respect to their application in combination with IC. Instrumental aspects including hardware requirements, configuration of membrane separation units and membrane characteristics are presented. Operation in batch and flow-through mode is described with emphasis on the latter to in-line coupling with IC, permitting fully automated operation. Attention is also drawn to dialysis probes and microdialysis both providing options for in-situ measurements with inherent selective sampling of analytes and sample preparation. The respective features of the various techniques are outlined with respect to the possibilities of matrix removal and selectivity enhancement. In this article, we provide examples of application of the diverse membrane separation techniques and discuss the benefits and limitations thereof.

  1. Selected configuration interaction method using sampled first-order corrections to wave functions

    NASA Astrophysics Data System (ADS)

    Ohtsuka, Yuhki; Hasegawa, Jun-ya

    2017-07-01

    A new selected configuration interaction (CI) method was proposed for the potential energy surfaces of quasi-degenerate and excited states. Slater determinants are generated by sampling the first-order corrections to the target-state wave functions using the quantum Monte Carlo method in determinant space. As in the Monte Carlo (MC) CI method, the wave function is improved at each iteration by generating new determinants and applying a pruning step. Compared to the random generation in the MCCI calculations, the number of iterations before convergence is significantly reduced. Regarding the potential energy curves of the ground and excited states of C2, the non-parallelity errors were sufficiently small, thus indicating the method's applicability to the calculations of potential energy surfaces.

  2. Estimation of the transition/transversion rate bias and species sampling.

    PubMed

    Yang, Z; Yoder, A D

    1999-03-01

    The transition/transversion (ti/tv) rate ratios are estimated by pairwise sequence comparison and joint likelihood analysis using mitochondrial cytochrome b genes of 28 primate species, representing both the Strepsirrhini (lemurs and lories) and the Anthropoidea (monkeys, apes, and humans). Pairwise comparison reveals a strong negative correlation between estimates of the ti/tv ratio and the sequence distance, even when both are corrected for multiple substitutions. The maximum-likelihood estimate of the ti/tv ratio changes with the species included in the analysis. The ti/tv bias within the lemuriform taxa is found to be as strong as in the anthropoids, in contradiction to an earlier study which sampled only one lemuriform. Simulations show the surprising result that both the pairwise correction method and the joint likelihood analysis tend to overcorrect for multiple substitutions and overestimate the ti/tv ratio, especially at low sequence divergence. The bias, however, is not large enough to account for the observed patterns. Nucleotide frequency biases, variation of substitution rates among sites, and different evolutionary dynamics at the three codon positions can be ruled out as possible causes. The likelihood-ratio test suggests that the ti/tv rate ratios may be variable among evolutionary lineages. Without any biological evidence for such a variation, however, we are left with no plausible explanations for the observed patterns other than a possible saturation effect due to the unrealistic nature of the model assumed.

  3. The Effects of Sampling Bias and Model Complexity on the Predictive Performance of MaxEnt Species Distribution Models

    PubMed Central

    Syfert, Mindy M.; Smith, Matthew J.; Coomes, David A.

    2013-01-01

    Species distribution models (SDMs) trained on presence-only data are frequently used in ecological research and conservation planning. However, users of SDM software are faced with a variety of options, and it is not always obvious how selecting one option over another will affect model performance. Working with MaxEnt software and with tree fern presence data from New Zealand, we assessed whether (a) choosing to correct for geographical sampling bias and (b) using complex environmental response curves have strong effects on goodness of fit. SDMs were trained on tree fern data, obtained from an online biodiversity data portal, with two sources that differed in size and geographical sampling bias: a small, widely-distributed set of herbarium specimens and a large, spatially clustered set of ecological survey records. We attempted to correct for geographical sampling bias by incorporating sampling bias grids in the SDMs, created from all georeferenced vascular plants in the datasets, and explored model complexity issues by fitting a wide variety of environmental response curves (known as “feature types” in MaxEnt). In each case, goodness of fit was assessed by comparing predicted range maps with tree fern presences and absences using an independent national dataset to validate the SDMs. We found that correcting for geographical sampling bias led to major improvements in goodness of fit, but did not entirely resolve the problem: predictions made with clustered ecological data were inferior to those made with the herbarium dataset, even after sampling bias correction. We also found that the choice of feature type had negligible effects on predictive performance, indicating that simple feature types may be sufficient once sampling bias is accounted for. Our study emphasizes the importance of reducing geographical sampling bias, where possible, in datasets used to train SDMs, and the effectiveness and essentialness of sampling bias correction within MaxEnt. PMID

  4. The effects of sampling bias and model complexity on the predictive performance of MaxEnt species distribution models.

    PubMed

    Syfert, Mindy M; Smith, Matthew J; Coomes, David A

    2013-01-01

    Species distribution models (SDMs) trained on presence-only data are frequently used in ecological research and conservation planning. However, users of SDM software are faced with a variety of options, and it is not always obvious how selecting one option over another will affect model performance. Working with MaxEnt software and with tree fern presence data from New Zealand, we assessed whether (a) choosing to correct for geographical sampling bias and (b) using complex environmental response curves have strong effects on goodness of fit. SDMs were trained on tree fern data, obtained from an online biodiversity data portal, with two sources that differed in size and geographical sampling bias: a small, widely-distributed set of herbarium specimens and a large, spatially clustered set of ecological survey records. We attempted to correct for geographical sampling bias by incorporating sampling bias grids in the SDMs, created from all georeferenced vascular plants in the datasets, and explored model complexity issues by fitting a wide variety of environmental response curves (known as "feature types" in MaxEnt). In each case, goodness of fit was assessed by comparing predicted range maps with tree fern presences and absences using an independent national dataset to validate the SDMs. We found that correcting for geographical sampling bias led to major improvements in goodness of fit, but did not entirely resolve the problem: predictions made with clustered ecological data were inferior to those made with the herbarium dataset, even after sampling bias correction. We also found that the choice of feature type had negligible effects on predictive performance, indicating that simple feature types may be sufficient once sampling bias is accounted for. Our study emphasizes the importance of reducing geographical sampling bias, where possible, in datasets used to train SDMs, and the effectiveness and essentialness of sampling bias correction within MaxEnt.

  5. Correcting Type Ia Supernova Distances for Selection Biases and Contamination in Photometrically Identified Samples

    NASA Astrophysics Data System (ADS)

    Kessler, R.; Scolnic, D.

    2017-02-01

    We present a new technique to create a bin-averaged Hubble diagram (HD) from photometrically identified SN Ia data. The resulting HD is corrected for selection biases and contamination from core-collapse (CC) SNe, and can be used to infer cosmological parameters. This method, called “BEAMS with Bias Corrections” (BBC), includes two fitting stages. The first BBC fitting stage uses a posterior distribution that includes multiple SN likelihoods, a Monte Carlo simulation to bias-correct the fitted SALT-II parameters, and CC probabilities determined from a machine-learning technique. The BBC fit determines (1) a bin-averaged HD (average distance versus redshift), and (2) the nuisance parameters α and β, which multiply the stretch and color (respectively) to standardize the SN brightness. In the second stage, the bin-averaged HD is fit to a cosmological model where priors can be imposed. We perform high-precision tests of the BBC method by simulating large (150,000 event) data samples corresponding to the Dark Energy Survey Supernova Program. Our tests include three models of intrinsic scatter, each with two different CC rates. In the BBC fit, the SALT-II nuisance parameters α and β are recovered to within 1% of their true values. In the cosmology fit, we determine the dark energy equation of state parameter w using a fixed value of {{{Ω }}}{{M}} as a prior: averaging over all six tests based on 6 × 150,000 = 900,000 SNe, there is a small w-bias of 0.006+/- 0.002. Finally, the BBC fitting code is publicly available in the SNANA package.

  6. Analytical validation of serum proteomic profiling for diagnosis of prostate cancer: sources of sample bias.

    PubMed

    McLerran, Dale; Grizzle, William E; Feng, Ziding; Bigbee, William L; Banez, Lionel L; Cazares, Lisa H; Chan, Daniel W; Diaz, Jose; Izbicka, Elzbieta; Kagan, Jacob; Malehorn, David E; Malik, Gunjan; Oelschlager, Denise; Partin, Alan; Randolph, Timothy; Rosenzweig, Nicole; Srivastava, Shiv; Srivastava, Sudhir; Thompson, Ian M; Thornquist, Mark; Troyer, Dean; Yasui, Yutaka; Zhang, Zhen; Zhu, Liu; Semmes, O John

    2008-01-01

    This report and a companion report describe a validation of the ability of serum proteomic profiling via SELDI-TOF mass spectrometry to detect prostatic cancer. Details of this 3-stage process have been described. This report describes the development of the algorithm and results of the blinded test for stage 1. We derived the decision algorithm used in this study from the analysis of serum samples from patients with prostate cancer (n = 181) and benign prostatic hyperplasia (BPH) (n = 143) and normal controls (n = 220). We also derived a validation test set from a separate, geographically diverse set of serum samples from 42 prostate cancer patients and 42 controls without prostate cancer. Aliquots were subjected to randomization and blinded analysis, and data from each laboratory site were subjected to the decision algorithm and decoded. Using the data collected from the validation test set, the decision algorithm was unsuccessful in separating cancer from controls with any predictive utility. Analysis of the experimental data revealed potential sources of bias. The ability of the decision algorithm to successfully differentiate between prostate cancer, BPH, and control samples using data derived from serum protein profiling was compromised by bias.

  7. Some comments on Anderson and Pospahala's correction of bias in line transect sampling

    USGS Publications Warehouse

    Anderson, D.R.; Burnham, K.P.; Chain, B.R.

    1980-01-01

    ANDERSON and POSPAHALA (1970) investigated the estimation of wildlife population size using the belt or line transect sampling method and devised a correction for bias, thus leading to an estimator with interesting characteristics. This work was given a uniform mathematical framework in BURNHAM and ANDERSON (1976). In this paper we show that the ANDERSON-POSPAHALA estimator is optimal in the sense of being the (unique) best linear unbiased estimator within the class of estimators which are linear combinations of cell frequencies, provided certain assumptions are met.

  8. Anhysteretic and biased first magnetization curves for Finemet-type toroidal samples

    NASA Astrophysics Data System (ADS)

    Varga, L. K.; Kovács, Gy.; Takács, J.

    The anhysteretic and a set of biased first magnetization (BFMC) curves together with a set of first-order reversal curves (FORC) were measured and modeled by the hyperbolic T( x) model for a Finemet-type nanocrystalline toroidal sample with a round hysteresis loop. Similar to the FORC diagram, a "fingerprint"-like distribution has been obtained from a set of BFMC curves using the mixed second-derivate method of Pike. It is concluded that while the FORC diagram gives the distribution of coercive fields (or Preisach distribution), the BFMC diagram gives the distribution of the critical field where the domain wall magnetization become unstable and split up.

  9. Estimating the effect of recurrent infectious diseases on nutritional status: sampling frequency, sample-size, and bias.

    PubMed

    Schmidt, Wolf-Peter; Genser, Bernd; Luby, Stephen P; Chalabi, Zaid

    2011-08-01

    There is an ongoing interest in studying the effect of common recurrent infections and conditions, such as diarrhoea, respiratory infections, and fever, on the nutritional status of children at risk of malnutrition. Epidemiological studies exploring this association need to measure infections with sufficient accuracy to minimize bias in the effect estimates. A versatile model of common recurrent infections was used for exploring how many repeated measurements of disease are required to maximize the power and logistical efficiency of studies investigating the effect of infectious diseases on malnutrition without compromising the validity of the estimates. Depending on the prevalence and distribution of disease within a population, 15-30 repeat measurements per child over one year should be sufficient to provide unbiased estimates of the association between infections and nutritional status. Less-frequent measurements lead to a bias in the effect size towards zero, especially if disease is rare. In contrast, recall error can lead to exaggerated effect sizes. Recall periods of three days or shorter may be preferable compared to longer recall periods. The results showed that accurate estimation of the association between recurrent infections and nutritional status required closer follow-up of study participants than studies using recurrent infections as an outcome measure. The findings of the study provide guidance for choosing an appropriate sampling strategy to explore this association.

  10. Sample Size Requirements for Structural Equation Models: An Evaluation of Power, Bias, and Solution Propriety.

    PubMed

    Wolf, Erika J; Harrington, Kelly M; Clark, Shaunna L; Miller, Mark W

    2013-12-01

    Determining sample size requirements for structural equation modeling (SEM) is a challenge often faced by investigators, peer reviewers, and grant writers. Recent years have seen a large increase in SEMs in the behavioral science literature, but consideration of sample size requirements for applied SEMs often relies on outdated rules-of-thumb. This study used Monte Carlo data simulation techniques to evaluate sample size requirements for common applied SEMs. Across a series of simulations, we systematically varied key model properties, including number of indicators and factors, magnitude of factor loadings and path coefficients, and amount of missing data. We investigated how changes in these parameters affected sample size requirements with respect to statistical power, bias in the parameter estimates, and overall solution propriety. Results revealed a range of sample size requirements (i.e., from 30 to 460 cases), meaningful patterns of association between parameters and sample size, and highlight the limitations of commonly cited rules-of-thumb. The broad "lessons learned" for determining SEM sample size requirements are discussed.

  11. Cross-validation under separate sampling: strong bias and how to correct it.

    PubMed

    Braga-Neto, Ulisses M; Zollanvari, Amin; Dougherty, Edward R

    2014-12-01

    It is commonly assumed in pattern recognition that cross-validation error estimation is 'almost unbiased' as long as the number of folds is not too small. While this is true for random sampling, it is not true with separate sampling, where the populations are independently sampled, which is a common situation in bioinformatics. We demonstrate, via analytical and numerical methods, that classical cross-validation can have strong bias under separate sampling, depending on the difference between the sampling ratios and the true population probabilities. We propose a new separate-sampling cross-validation error estimator, and prove that it satisfies an 'almost unbiased' theorem similar to that of random-sampling cross-validation. We present two case studies with previously published data, which show that the results can change drastically if the correct form of cross-validation is used. The source code in C++, along with the Supplementary Materials, is available at: http://gsp.tamu.edu/Publications/supplementary/zollanvari13/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  12. Active Learning to Overcome Sample Selection Bias: Application to Photometric Variable Star Classification

    NASA Astrophysics Data System (ADS)

    Richards, Joseph W.; Starr, Dan L.; Brink, Henrik; Miller, Adam A.; Bloom, Joshua S.; Butler, Nathaniel R.; James, J. Berian; Long, James P.; Rice, John

    2012-01-01

    Despite the great promise of machine-learning algorithms to classify and predict astrophysical parameters for the vast numbers of astrophysical sources and transients observed in large-scale surveys, the peculiarities of the training data often manifest as strongly biased predictions on the data of interest. Typically, training sets are derived from historical surveys of brighter, more nearby objects than those from more extensive, deeper surveys (testing data). This sample selection bias can cause catastrophic errors in predictions on the testing data because (1) standard assumptions for machine-learned model selection procedures break down and (2) dense regions of testing space might be completely devoid of training data. We explore possible remedies to sample selection bias, including importance weighting, co-training, and active learning (AL). We argue that AL—where the data whose inclusion in the training set would most improve predictions on the testing set are queried for manual follow-up—is an effective approach and is appropriate for many astronomical applications. For a variable star classification problem on a well-studied set of stars from Hipparcos and Optical Gravitational Lensing Experiment, AL is the optimal method in terms of error rate on the testing data, beating the off-the-shelf classifier by 3.4% and the other proposed methods by at least 3.0%. To aid with manual labeling of variable stars, we developed a Web interface which allows for easy light curve visualization and querying of external databases. Finally, we apply AL to classify variable stars in the All Sky Automated Survey, finding dramatic improvement in our agreement with the ASAS Catalog of Variable Stars, from 65.5% to 79.5%, and a significant increase in the classifier's average confidence for the testing set, from 14.6% to 42.9%, after a few AL iterations.

  13. ACTIVE LEARNING TO OVERCOME SAMPLE SELECTION BIAS: APPLICATION TO PHOTOMETRIC VARIABLE STAR CLASSIFICATION

    SciTech Connect

    Richards, Joseph W.; Starr, Dan L.; Miller, Adam A.; Bloom, Joshua S.; Butler, Nathaniel R.; Berian James, J.; Brink, Henrik; Long, James P.; Rice, John

    2012-01-10

    Despite the great promise of machine-learning algorithms to classify and predict astrophysical parameters for the vast numbers of astrophysical sources and transients observed in large-scale surveys, the peculiarities of the training data often manifest as strongly biased predictions on the data of interest. Typically, training sets are derived from historical surveys of brighter, more nearby objects than those from more extensive, deeper surveys (testing data). This sample selection bias can cause catastrophic errors in predictions on the testing data because (1) standard assumptions for machine-learned model selection procedures break down and (2) dense regions of testing space might be completely devoid of training data. We explore possible remedies to sample selection bias, including importance weighting, co-training, and active learning (AL). We argue that AL-where the data whose inclusion in the training set would most improve predictions on the testing set are queried for manual follow-up-is an effective approach and is appropriate for many astronomical applications. For a variable star classification problem on a well-studied set of stars from Hipparcos and Optical Gravitational Lensing Experiment, AL is the optimal method in terms of error rate on the testing data, beating the off-the-shelf classifier by 3.4% and the other proposed methods by at least 3.0%. To aid with manual labeling of variable stars, we developed a Web interface which allows for easy light curve visualization and querying of external databases. Finally, we apply AL to classify variable stars in the All Sky Automated Survey, finding dramatic improvement in our agreement with the ASAS Catalog of Variable Stars, from 65.5% to 79.5%, and a significant increase in the classifier's average confidence for the testing set, from 14.6% to 42.9%, after a few AL iterations.

  14. Low-bias phosphopeptide enrichment from scarce samples using plastic antibodies

    PubMed Central

    Chen, Jing; Shinde, Sudhirkumar; Koch, Markus-Hermann; Eisenacher, Martin; Galozzi, Sara; Lerari, Thilo; Barkovits, Katalin; Subedi, Prabal; Krüger, Rejko; Kuhlmann, Katja; Sellergren, Börje; Helling, Stefan; Marcus, Katrin

    2015-01-01

    Phosphospecific enrichment techniques and mass spectrometry (MS) are essential tools for comprehending the cellular phosphoproteome. Here, we report a fast and simple approach for low sequence-bias phosphoserine (pS) peptide capture and enrichment that is compatible with low biological or clinical sample input. The approach exploits molecularly imprinted polymers (MIPs, “plastic antibodies”) featuring tight neutral binding sites for pS or pY that are capable of cross-reacting with phosphopeptides of protein proteolytic digests. The versatility of the resulting method was demonstrated with small samples of whole-cell lysate from human embryonic kidney (HEK) 293T cells, human neuroblastoma SH-SY5Y cells, mouse brain or human cerebrospinal fluid (CSF). Following pre-fractionation of trypsinized proteins by strong cation exchange (SCX) chromatography, pS-MIP enrichment led to the identification of 924 phosphopeptides in the HEK 293T whole-cell lysate, exceeding the number identified by TiO2-based enrichment (230). Moreover, the phosphopeptides were extracted with low sequence bias and showed no evidence for the characteristic preference of TiO2 for acidic amino acids (aspartic and glutamic acid). Applying the method to human CSF led to the discovery of 47 phosphopeptides belonging to 24 proteins and revealed three previously unknown phosphorylation sites. PMID:26126808

  15. Analytical bias among different gas chromatographic approaches using standard BTX gases and exhaust samples.

    PubMed

    Kim, Ki-Hyun; Pandey, Sudhir Kumar; Pal, Raktim

    2009-02-01

    In this study, the analytical compatibility of the gas chromatographic (GC) approach was evaluated through a cross-calibration exercise. To this end, three aromatic volatile organic compounds (VOCs: benzene, toluene, and p-xylene (BTX)) were simultaneously analyzed with four individual instrumental setups (type I = GC with MS plus solid phase microextraction (SPME) method, II = GC with flame ionization detection (FID) plus SPME, III = fast GC-FID plus SPME, and IV = GC-FID plus air server/thermal desorption (AS/TD) method). A comparison of basic quality assurance (QA) data revealed considerable differences in DL values among the methods with moderate variabilities in the intercompound sensitivity. In light of the differences in detection properties, the analytical bias involved for each methodological approach was assessed by the relative relationship between analytes and basic operating conditions. The results suggest that the analysis of environmental samples at ultra-low concentration levels (at or below ppb level) can be subject to diverse sources of bias. Although detection properties of target compounds seem to be affected by the combined effects of various factors, changes in the sample concentration levels were seen to be the most consistent under the experimental setups analyzed in this study.

  16. Small sample bias in the gamma frailty model for univariate survival.

    PubMed

    Barker, Peter; Henderson, Robin

    2005-06-01

    The gamma frailty model is a natural extension of the Cox proportional hazards model in survival analysis. Because the frailties are unobserved, an E-M approach is often used for estimation. Such an approach is shown to lead to finite sample underestimation of the frailty variance, with the corresponding regression parameters also being underestimated as a result. For the univariate case, we investigate the source of the bias with simulation studies and a complete enumeration. The rank-based E-M approach, we note, only identifies frailty through the order in which failures occur; additional frailty which is evident in the survival times is ignored, and as a result the frailty variance is underestimated. An adaption of the standard E-M approach is suggested, whereby the non-parametric Breslow estimate is replaced by a local likelihood formulation for the baseline hazard which allows the survival times themselves to enter the model. Simulations demonstrate that this approach substantially reduces the bias, even at small sample sizes. The method developed is applied to survival data from the North West Regional Leukaemia Register.

  17. Sea level, dinosaur diversity and sampling biases: investigating the 'common cause' hypothesis in the terrestrial realm.

    PubMed

    Butler, Richard J; Benson, Roger B J; Carrano, Matthew T; Mannion, Philip D; Upchurch, Paul

    2011-04-22

    The fossil record is our primary window onto the diversification of ancient life, but there are widespread concerns that sampling biases may distort observed palaeodiversity counts. Such concerns have been reinforced by numerous studies that found correlations between measures of sampling intensity and observed diversity. However, correlation does not necessarily mean that sampling controls observed diversity: an alternative view is that both sampling and diversity may be driven by some common factor (e.g. variation in continental flooding driven by sea level). The latter is known as the 'common cause' hypothesis. Here, we present quantitative analyses of the relationships between dinosaur diversity, sampling of the dinosaur fossil record, and changes in continental flooding and sea level, providing new insights into terrestrial common cause. Although raw data show significant correlations between continental flooding/sea level and both observed diversity and sampling, these correlations do not survive detrending or removal of short-term autocorrelation. By contrast, the strong correlation between diversity and sampling is robust to various data transformations. Correlations between continental flooding/sea level and taxic diversity/sampling result from a shared upward trend in all data series, and short-term changes in continental flooding/sea level and diversity/sampling do not correlate. The hypothesis that global dinosaur diversity is tied to sea-level fluctuations is poorly supported, and terrestrial common cause is unsubstantiated as currently conceived. Instead, we consider variation in sampling to be the preferred null hypothesis for short-term diversity variation in the Mesozoic terrestrial realm.

  18. An interaction energy driven biased sampling technique: A faster route to ionization spectra in condensed phase.

    PubMed

    Bose, Samik; Ghosh, Debashree

    2017-10-05

    We introduce a computationally efficient approach for calculating spectroscopic properties, such as ionization energies (IEs) in the condensed phase. Discrete quantum mechanical/molecular mechanical (QM/MM) approaches for spectroscopic properties in a dynamic system, such as aqueous solution, need a large sample space to obtain converged estimates, especially for the cases where particle (electron) number is not conserved, such as IEs or electron affinities (EAs). We devise a biased sampling technique based on an approximate estimate of interaction energy between the solute and solvent, that accelerates the convergence and therefore, reduces the computational cost significantly. The approximate interaction energy also provides a good measure of the spectral width of the chromophores in the condensed phase. This technique has been tested and benchmarked for (i) phenol, (ii) HBDI anion (hydroxybenzylidene dimethyl imidazolinone), and (iii) thymine in water. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  19. Control of ion gyroscale fluctuations via electrostatic biasing and sheared E×B flow in the C-2 field reversed configuration

    NASA Astrophysics Data System (ADS)

    Schmitz, L.; Ruskov, E.; Deng, B. H.; Binderbauer, M.; Tajima, T.; Gota, H.; Tuszewski, M.

    2016-03-01

    Control of radial particle and thermal transport is instrumental for achieving and sustaining well-confined high-β plasma in a Field-Reversed Configuration (FRC). Radial profiles of low frequency ion gyro-scale density fluctuations (0.5≤kρs≤40), consistent with drift- or drift-interchange modes, have been measured in the scrape-off layer (SOL) and core of the C-2 Field-Reversed Configuration (FRC), together with the toroidal E×B velocity. It is shown here that axial electrostatic SOL biasing controls and reduces gyro-scale density fluctuations, resulting in very low FRC core fluctuation levels. When the radial E×B flow shearing rate decreases below the turbulence decorrelation rate, fluctuation levels increase substantially, concomitantly with onset of the n=2 instability and rapid loss of diamagnetism. Low turbulence levels, improved energy/particle confinement and substantially increased FRC life times are achieved when E×B shear near the separatrix is maintained via axial SOL biasing using an annular washer gun.

  20. Low-mass molecular dynamics simulation: A simple and generic technique to enhance configurational sampling

    SciTech Connect

    Pang, Yuan-Ping

    2014-09-26

    Highlights: • Reducing atomic masses by 10-fold vastly improves sampling in MD simulations. • CLN025 folded in 4 of 10 × 0.5-μs MD simulations when masses were reduced by 10-fold. • CLN025 folded as early as 96.2 ns in 1 of the 4 simulations that captured folding. • CLN025 did not fold in 10 × 0.5-μs MD simulations when standard masses were used. • Low-mass MD simulation is a simple and generic sampling enhancement technique. - Abstract: CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its native conformation in a classical, all-atom, and isothermal–isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277 K and 1 atm with the first folding event occurring as early as 66.1 ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal–isobaric MD simulations performed on commodity computers—an important step forward in quantitative biology.

  1. Estimates of the average strength of natural selection are not inflated by sampling error or publication bias.

    PubMed

    Knapczyk, Frances N; Conner, Jeffrey K

    2007-10-01

    Kingsolver et al.'s review of phenotypic selection gradients from natural populations provided a glimpse of the form and strength of selection in nature and how selection on different organisms and traits varies. Because this review's underlying database could be a key tool for answering fundamental questions concerning natural selection, it has spawned discussion of potential biases inherent in the review process. Here, we explicitly test for two commonly discussed sources of bias: sampling error and publication bias. We model the relationship between variance among selection gradients and sample size that sampling error produces by subsampling large empirical data sets containing measurements of traits and fitness. We find that this relationship was not mimicked by the review data set and therefore conclude that sampling error does not bias estimations of the average strength of selection. Using graphical tests, we find evidence for bias against publishing weak estimates of selection only among very small studies (N<38). However, this evidence is counteracted by excess weak estimates in larger studies. Thus, estimates of average strength of selection from the review are less biased than is often assumed. Devising and conducting straightforward tests for different biases allows concern to be focused on the most troublesome factors.

  2. How many dinosaur species were there? Fossil bias and true richness estimated using a Poisson sampling model.

    PubMed

    Starrfelt, Jostein; Liow, Lee Hsiang

    2016-04-05

    The fossil record is a rich source of information about biological diversity in the past. However, the fossil record is not only incomplete but has also inherent biases due to geological, physical, chemical and biological factors. Our knowledge of past life is also biased because of differences in academic and amateur interests and sampling efforts. As a result, not all individuals or species that lived in the past are equally likely to be discovered at any point in time or space. To reconstruct temporal dynamics of diversity using the fossil record, biased sampling must be explicitly taken into account. Here, we introduce an approach that uses the variation in the number of times each species is observed in the fossil record to estimate both sampling bias and true richness. We term our technique TRiPS (True Richness estimated using a Poisson Sampling model) and explore its robustness to violation of its assumptions via simulations. We then venture to estimate sampling bias and absolute species richness of dinosaurs in the geological stages of the Mesozoic. Using TRiPS, we estimate that 1936 (1543-2468) species of dinosaurs roamed the Earth during the Mesozoic. We also present improved estimates of species richness trajectories of the three major dinosaur clades: the sauropodomorphs, ornithischians and theropods, casting doubt on the Jurassic-Cretaceous extinction event and demonstrating that all dinosaur groups are subject to considerable sampling bias throughout the Mesozoic.

  3. How many dinosaur species were there? Fossil bias and true richness estimated using a Poisson sampling model

    PubMed Central

    Starrfelt, Jostein; Liow, Lee Hsiang

    2016-01-01

    The fossil record is a rich source of information about biological diversity in the past. However, the fossil record is not only incomplete but has also inherent biases due to geological, physical, chemical and biological factors. Our knowledge of past life is also biased because of differences in academic and amateur interests and sampling efforts. As a result, not all individuals or species that lived in the past are equally likely to be discovered at any point in time or space. To reconstruct temporal dynamics of diversity using the fossil record, biased sampling must be explicitly taken into account. Here, we introduce an approach that uses the variation in the number of times each species is observed in the fossil record to estimate both sampling bias and true richness. We term our technique TRiPS (True Richness estimated using a Poisson Sampling model) and explore its robustness to violation of its assumptions via simulations. We then venture to estimate sampling bias and absolute species richness of dinosaurs in the geological stages of the Mesozoic. Using TRiPS, we estimate that 1936 (1543–2468) species of dinosaurs roamed the Earth during the Mesozoic. We also present improved estimates of species richness trajectories of the three major dinosaur clades: the sauropodomorphs, ornithischians and theropods, casting doubt on the Jurassic–Cretaceous extinction event and demonstrating that all dinosaur groups are subject to considerable sampling bias throughout the Mesozoic. PMID:26977060

  4. Low-mass molecular dynamics simulation: a simple and generic technique to enhance configurational sampling.

    PubMed

    Pang, Yuan-Ping

    2014-09-26

    CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its native conformation in a classical, all-atom, and isothermal-isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277K and 1atm with the first folding event occurring as early as 66.1ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal-isobaric MD simulations performed on commodity computers-an important step forward in quantitative biology. Copyright © 2014 The Author. Published by Elsevier Inc. All rights reserved.

  5. Sample selection bias and presence-only distribution models: implications for background and pseudo-absence data.

    PubMed

    Phillips, Steven J; Dudík, Miroslav; Elith, Jane; Graham, Catherine H; Lehmann, Anthony; Leathwick, John; Ferrier, Simon

    2009-01-01

    Most methods for modeling species distributions from occurrence records require additional data representing the range of environmental conditions in the modeled region. These data, called background or pseudo-absence data, are usually drawn at random from the entire region, whereas occurrence collection is often spatially biased toward easily accessed areas. Since the spatial bias generally results in environmental bias, the difference between occurrence collection and background sampling may lead to inaccurate models. To correct the estimation, we propose choosing background data with the same bias as occurrence data. We investigate theoretical and practical implications of this approach. Accurate information about spatial bias is usually lacking, so explicit biased sampling of background sites may not be possible. However, it is likely that an entire target group of species observed by similar methods will share similar bias. We therefore explore the use of all occurrences within a target group as biased background data. We compare model performance using target-group background and randomly sampled background on a comprehensive collection of data for 226 species from diverse regions of the world. We find that target-group background improves average performance for all the modeling methods we consider, with the choice of background data having as large an effect on predictive performance as the choice of modeling method. The performance improvement due to target-group background is greatest when there is strong bias in the target-group presence records. Our approach applies to regression-based modeling methods that have been adapted for use with occurrence data, such as generalized linear or additive models and boosted regression trees, and to Maxent, a probability density estimation method. We argue that increased awareness of the implications of spatial bias in surveys, and possible modeling remedies, will substantially improve predictions of species

  6. Bias field tunable magnetic configuration and magnetization dynamics in Ni80Fe20 nano-cross structures with varying arm length

    NASA Astrophysics Data System (ADS)

    Adhikari, K.; Choudhury, S.; Mandal, R.; Barman, S.; Otani, Y.; Barman, A.

    2017-01-01

    Ferromagnetic nano-cross structures promise exotic static magnetic configurations and very rich and tunable magnetization dynamics leading towards potential applications in magnetic logic and communication devices. Here, we report an experimental study of external magnetic field tunable static magnetic configurations and magnetization dynamics in Ni80Fe20 nano-cross structures with varying arm lengths (L). Broadband ferromagnetic resonance measurements showed a strong variation in the number of spin-wave (SW) modes and mode frequencies (f) with bias field magnitude (H). Simulated static magnetic configurations and SW mode profiles explain the rich variation of the SW spectra, including mode softening, mode crossover, mode splitting, and mode merging. Such variation of SW spectra is further modified by the size of the nano-cross. Remarkably, with decreasing arm length of nano-cross structures, the onion magnetization ground state becomes more stable. Calculated magnetostatic field distributions support the above observations and revealed the non-collective nature of the dynamics in closely packed nano-cross structures. The latter is useful for their possible applications in magnetic storage and memory devices.

  7. [Evaluation of visual attentional biases in a sample of university smokers].

    PubMed

    Morales Domínguez, Zaira; Pascual Orts, Luis Miguel; Garrido Muñoz de Arenillas, Rocío

    2013-01-01

    The tobacco consumption continues being a worrying problem due to the negative consequences in the health. At presents, strategies of prevention based on the persuasion across clue pictures are used, which need to attract the attention of the smoker in order that they are effective. Nevertheless, the number of experimental studies in Spain on attentional biases in smokers is very limited. For it, in this study the aim was to verify the presence of visual attentional biases using the dot probe task in university smokers, stage where the smoking habit is consolidated. The sample was constituted by 337 students of the University of Huelva, with ages between 17 and 30 years. The participation was voluntary and the participants signed an informed assent. 135 subjects presented consumption history, which were distributed, according to classification of the WHO, in daily smokers, occasional smokers and former smokers. A experimental Ex post facto prospective design was used. The results showed that the smokers group was significantly later time to respond to the clue located in the same place that the tobacco picture than the group of not smokers. This shows that the smokers presented more difficulty to disconnect the attention towards smoking cues than not smokers.

  8. Screening Items for Bias: An Empirical Comparison of the Performance of Three Indices in Small Samples of Examinees.

    ERIC Educational Resources Information Center

    Kromrey, Jeffrey D.; Parshall, Cynthia G.

    A Monte Carlo study was conducted to compare the performance of three statistical indices of test item bias in small samples of examinees. The statistical indices compared were the Delta method, the Mantel-Haenszel (MH) method, and the Standardization method. Sample sizes of 50, 100, and 200 were examined. One thousand samples of each size were…

  9. The Perils of Straying from Protocol: Sampling Bias and Interviewer Effects

    PubMed Central

    Ngongo, Carrie J.; Frick, Kevin D.; Hightower, Allen W.; Mathingau, Florence Alice; Burke, Heather; Breiman, Robert F.

    2015-01-01

    Fidelity to research protocol is critical. In a contingent valuation study in an informal urban settlement in Nairobi, Kenya, participants responded differently to the three trained interviewers. Interviewer effects were present during the survey pilot, then magnified at the start of the main survey after a seemingly slight adaptation of the survey sampling protocol allowed interviewers to speak with the “closest neighbor” in the event that no one was home at a selected household. This slight degree of interviewer choice led to inferred sampling bias. Multinomial logistic regression and post-estimation tests revealed that the three interviewers’ samples differed significantly from one another according to six demographic characteristics. The two female interviewers were 2.8 and 7.7 times less likely to talk with respondents of low socio-economic status than the male interviewer. Systematic error renders it impossible to determine which of the survey responses might be “correct.” This experience demonstrates why researchers must take care to strictly follow sampling protocols, consistently train interviewers, and monitor responses by interview to ensure similarity between interviewers’ groups and produce unbiased estimates of the parameters of interest. PMID:25693077

  10. Comparison of Relative Bias, Precision, and Efficiency of Sampling Methods for Natural Enemies of Soybean Aphid (Hemiptera: Aphididae).

    PubMed

    Bannerman, J A; Costamagna, A C; McCornack, B P; Ragsdale, D W

    2015-06-01

    Generalist natural enemies play an important role in controlling soybean aphid, Aphis glycines (Hemiptera: Aphididae), in North America. Several sampling methods are used to monitor natural enemy populations in soybean, but there has been little work investigating their relative bias, precision, and efficiency. We compare five sampling methods: quadrats, whole-plant counts, sweep-netting, walking transects, and yellow sticky cards to determine the most practical methods for sampling the three most prominent species, which included Harmonia axyridis (Pallas), Coccinella septempunctata L. (Coleoptera: Coccinellidae), and Orius insidiosus (Say) (Hemiptera: Anthocoridae). We show an important time by sampling method interaction indicated by diverging community similarities within and between sampling methods as the growing season progressed. Similarly, correlations between sampling methods for the three most abundant species over multiple time periods indicated differences in relative bias between sampling methods and suggests that bias is not consistent throughout the growing season, particularly for sticky cards and whole-plant samples. Furthermore, we show that sticky cards produce strongly biased capture rates relative to the other four sampling methods. Precision and efficiency differed between sampling methods and sticky cards produced the most precise (but highly biased) results for adult natural enemies, while walking transects and whole-plant counts were the most efficient methods for detecting coccinellids and O. insidiosus, respectively. Based on bias, precision, and efficiency considerations, the most practical sampling methods for monitoring in soybean include walking transects for coccinellid detection and whole-plant counts for detection of small predators like O. insidiosus. Sweep-netting and quadrat samples are also useful for some applications, when efficiency is not paramount. © The Authors 2015. Published by Oxford University Press on behalf of

  11. Functional magnetic resonance imaging movers and shakers: does subject-movement cause sampling bias?

    PubMed

    Wylie, Glenn R; Genova, Helen; DeLuca, John; Chiaravalloti, Nancy; Sumowski, James F

    2014-01-01

    Head movement during functional magnetic resonance imaging (fMRI) degrades data quality. The effects of small movements can be ameliorated during data postprocessing, but data associated with severe movement is frequently discarded. In discarding these data, it is often assumed that head-movement is a source of random error, and that data can be discarded from subjects with severe movement without biasing the sample. We tested this assumption by examining whether head movement was related to task difficulty and cognitive status among persons with multiple sclerosis (MS). Thirty-four persons with MS were scanned while performing a working memory task with three levels of difficulty (the N-back task). Maximum movement (angle, shift) was estimated for each difficulty level. Cognitive status was assessed by combining performance on a working memory and processing speed task. An interaction was found between task difficulty and cognitive status (high vs. low cognitive ability): there was a linear increase in movement as task difficulty increased that was larger among subjects with lower cognitive ability. Analyses of the signal-to-noise ratio (SNR) confirmed that increases in movement degraded data quality. Similar, though far smaller, effects were found in a cohort of healthy control (HC) subjects. Therefore, discarding data with severe movement artifact may bias MS samples such that only those with less-severe cognitive impairment are included in the analyses. However, even if such data are not discarded outright, subjects who move more (MS and HC) will contribute less to the group-level results because of degraded SNR.

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

    PubMed

    Lunter, Dominique Jasmin

    2016-01-01

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

  13. Childhood trauma and negative memory bias as shared risk factors for psychopathology and comorbidity in a naturalistic psychiatric patient sample.

    PubMed

    Vrijsen, Janna N; van Amen, Camiel T; Koekkoek, Bauke; van Oostrom, Iris; Schene, Aart H; Tendolkar, Indira

    2017-06-01

    Both childhood trauma and negative memory bias are associated with the onset and severity level of several psychiatric disorders, such as depression and anxiety disorders. Studies on these risk factors, however, generally use homogeneous noncomorbid samples. Hence, studies in naturalistic psychiatric samples are lacking. Moreover, we know little about the quantitative relationship between the frequency of traumatic childhood events, strength of memory bias and number of comorbid psychiatric disorders; the latter being an index of severity. The current study examined the association of childhood trauma and negative memory bias with psychopathology in a large naturalistic psychiatric patient sample. Frequency of traumatic childhood events (emotional neglect, psychological-, physical- and sexual abuse) was assessed using a questionnaire in a sample of 252 adult psychiatric patients with no psychotic or bipolar-I disorder and no cognitive disorder as main diagnosis. Patients were diagnosed for DSM-IV Axis-I and Axis-II disorders using a structured clinical interview. This allowed for the assessment of comorbidity between disorders. Negative memory bias for verbal stimuli was measured using a computer task. Linear regression models revealed that the frequency of childhood trauma as well as negative memory bias was positively associated with psychiatric comorbidity, separately and above and beyond each other (all p < .01). The results indicate that childhood trauma and negative memory bias may be of importance for a broader spectrum of psychiatric diagnoses, besides the frequently studied affective disorders. Importantly, frequently experiencing traumatic events during childhood increases the risk of comorbid psychiatric disorders.

  14. Error and bias in under-5 mortality estimates derived from birth histories with small sample sizes.

    PubMed

    Dwyer-Lindgren, Laura; Gakidou, Emmanuela; Flaxman, Abraham; Wang, Haidong

    2013-07-26

    magnitude of expected error and bias in the estimates. Even with larger samples there is no clear best method to choose for analyzing birth history data. The methods that perform best overall are the same methods where performance is noticeably different at different levels of mortality and lengths of time prior to survey. At the same time, methods that perform more uniformly across levels of mortality and lengths of time prior to survey also tend to be among the worst performing overall.

  15. Goniochromatic and sparkle properties of effect pigmented samples in multidimensional configuration

    NASA Astrophysics Data System (ADS)

    Höpe, Andreas; Hauer, Kai-Olaf; Teichert, Sven; Hünerhoff, Dirk; Strothkämper, Christian

    2015-03-01

    The effects of goniochromatism and sparkle are gaining more and more interest for surface refinement applications driven by demanding requirements from such different branches as automotive, cosmetics, printing and packaging industry. The common background and intention in all of these implementations is improvement of the visual appearance of the related commercial products. Goniochromatic materials show strong angular-dependent reflection characteristics and hence a color impression depending on the effective spatial arrangement of illumination and observation relative to the surface of the artifact. Sparkle is a texture related effect giving a surface which is irradiated directionally, like direct sun light, a bright glittering effect, similar to twinkling stars at the night sky. The prototype for this new effect is the Xirallic® pigment of MERCK KGaA, Germany. The same pigment shows in diffuse irradiation, like on a cloudy day, a different visual effect called graininess (coarseness) which appears as a granular structure of the surface. Both effects were studied on especially manufactured samples of a dilution series in pigment concentration and a tonality series with carbon black. The experiments were carried out with the robot-based gonioreflectometer and integrating sphere facilities at Physikalisch-Technische Bundesanstalt (PTB) in multidimensional configurations of directional and diffuse irradiation. The research is part of the European Metrology Research Program (EMRP), which is a metrology-focused program of coordinated Research & Development (R&D) funded by the European Commission and participating countries within the European Association of National Metrology Institutes (EURAMET). More information and updated news concerning the project can be found on the xD-Reflect website http://www.xdreflect.eu/.

  16. Forms of attrition in a longitudinal study of religion and health in older adults and implications for sample bias

    PubMed Central

    Hayward, R. David; Krause, Neal

    2014-01-01

    The use of longitudinal designs in the field of religion and health makes it important to understand how attrition bias may affect findings in this area. This study examines attrition in a 4-wave, 8-year study of older adults. Attrition resulted in a sample biased towards more educated and more religiously-involved individuals. Conditional linear growth curve models found that trajectories of change for some variables differed among attrition categories. Ineligibles had worsening depression, declining control, and declining attendance. Mortality was associated with worsening religious coping styles. Refusers experienced worsening depression. Nevertheless, there was no evidence of bias in the key religion and health results. PMID:25257794

  17. Forms of Attrition in a Longitudinal Study of Religion and Health in Older Adults and Implications for Sample Bias.

    PubMed

    Hayward, R David; Krause, Neal

    2016-02-01

    The use of longitudinal designs in the field of religion and health makes it important to understand how attrition bias may affect findings in this area. This study examines attrition in a 4-wave, 8-year study of older adults. Attrition resulted in a sample biased toward more educated and more religiously involved individuals. Conditional linear growth curve models found that trajectories of change for some variables differed among attrition categories. Ineligibles had worsening depression, declining control, and declining attendance. Mortality was associated with worsening religious coping styles. Refusers experienced worsening depression. Nevertheless, there was no evidence of bias in the key religion and health results.

  18. Measurement of the Tracer Gradient and Sampling System Bias of the Hot Fuel Examination Facility Stack Air Monitoring System

    SciTech Connect

    Glissmeyer, John A.; Flaherty, Julia E.

    2011-07-20

    This report describes tracer gas uniformity and bias measurements made in the exhaust air discharge of the Hot Fuel Examination Facility at Idaho National Laboratory. The measurements were a follow-up on earlier measurements which indicated a lack of mixing of the two ventilation streams being discharged via a common stack. The lack of mixing is detrimental to the accuracy of air emission measurements. The lack of mixing was confirmed in these new measurements. The air sampling probe was found to be out of alignment and that was corrected. The suspected sampling bias in the air sample stream was disproved.

  19. The effects of social desirability response bias on STAXI-2 profiles in a clinical forensic sample.

    PubMed

    McEwan, Troy E; Davis, Michael R; MacKenzie, Rachel; Mullen, Paul E

    2009-11-01

    This study investigated the proposition that the 'State-trait anger expression inventory' (2nd ed.; STAXI-2) is susceptible to impression management (IM) and Self-Deceptive Enhancement (SDE) in clinical forensic populations. It was hypothesized that individuals engaging in IM would report significantly lower levels of trait anger, external expression of anger, and internal expression of anger on the STAXI-2. Those reporting above average SDE were predicted to claim higher levels of anger control. A between-groups design was used, comparing STAXI-2 scores of individuals who reported high levels of IM and SDE to those who did not. One-hundred and fifty-nine male patients of a community forensic mental health service, referred for assessment of stalking behaviours, completed the STAXI-2 and Paulhus Deception Scales (PDS). Individuals engaging in high levels of IM and SDE were compared to low scorers in regard to STAXI-2 scales using Mann-Whitney U tests. Individuals engaging in IM had significantly lower levels of reported trait anger, outward expression of anger, and inward expression of anger, and higher levels of anger control. Similar results were found with the SDE scale, although the magnitude of the effect was smaller and not apparent on all subscales. The STAXI-2 was vulnerable to social desirability response bias in this sample of forensic clients. Where the STAXI-2 is used as a basis for treatment recommendations and decisions, it should be administered and interpreted in conjunction with a recognized measure of such bias to improve validity.

  20. Evaluating vegetation effects on animal demographics: the role of plant phenology and sampling bias.

    PubMed

    Gibson, Daniel; Blomberg, Erik J; Sedinger, James S

    2016-04-24

    Plant phenological processes produce temporal variation in the height and cover of vegetation. Key aspects of animal life cycles, such as reproduction, often coincide with the growing season and therefore may inherently covary with plant growth. When evaluating the influence of vegetation variables on demographic rates, the decision about when to measure vegetation relative to the timing of demographic events is important to avoid confounding between the demographic rate of interest and vegetation covariates. Such confounding could bias estimated effect sizes or produce results that are entirely spurious. We investigated how the timing of vegetation sampling affected the modeled relationship between vegetation structure and nest survival of greater sage-grouse (Centrocercus urophasianus), using both simulated and observational data. We used the height of live grasses surrounding nests as an explanatory covariate, and analyzed its effect on daily nest survival. We compared results between models that included grass height measured at the time of nest fate (hatch or failure) with models where grass height was measured on a standardized date - that of predicted hatch date. Parameters linking grass height to nest survival based on measurements at nest fate produced more competitive models, but slope coefficients of grass height effects were biased high relative to truth in simulated scenarios. In contrast, measurements taken at predicted hatch date accurately predicted the influence of grass height on nest survival. Observational data produced similar results. Our results demonstrate the importance of properly considering confounding between demographic traits and plant phenology. Not doing so can produce results that are plausible, but ultimately inaccurate.

  1. Assessing total nitrogen in surface-water samples--precision and bias of analytical and computational methods

    USGS Publications Warehouse

    Rus, David L.; Patton, Charles J.; Mueller, David K.; Crawford, Charles G.

    2013-01-01

    The characterization of total-nitrogen (TN) concentrations is an important component of many surface-water-quality programs. However, three widely used methods for the determination of total nitrogen—(1) derived from the alkaline-persulfate digestion of whole-water samples (TN-A); (2) calculated as the sum of total Kjeldahl nitrogen and dissolved nitrate plus nitrite (TN-K); and (3) calculated as the sum of dissolved nitrogen and particulate nitrogen (TN-C)—all include inherent limitations. A digestion process is intended to convert multiple species of nitrogen that are present in the sample into one measureable species, but this process may introduce bias. TN-A results can be negatively biased in the presence of suspended sediment, and TN-K data can be positively biased in the presence of elevated nitrate because some nitrate is reduced to ammonia and is therefore counted twice in the computation of total nitrogen. Furthermore, TN-C may not be subject to bias but is comparatively imprecise. In this study, the effects of suspended-sediment and nitrate concentrations on the performance of these TN methods were assessed using synthetic samples developed in a laboratory as well as a series of stream samples. A 2007 laboratory experiment measured TN-A and TN-K in nutrient-fortified solutions that had been mixed with varying amounts of sediment-reference materials. This experiment identified a connection between suspended sediment and negative bias in TN-A and detected positive bias in TN-K in the presence of elevated nitrate. A 2009–10 synoptic-field study used samples from 77 stream-sampling sites to confirm that these biases were present in the field samples and evaluated the precision and bias of TN methods. The precision of TN-C and TN-K depended on the precision and relative amounts of the TN-component species used in their respective TN computations. Particulate nitrogen had an average variability (as determined by the relative standard deviation) of 13

  2. Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing.

    PubMed

    Guo, Feng; Zhang, Tong

    2013-05-01

    Standardization of DNA extraction is a fundamental issue of fidelity and comparability in investigations of environmental microbial communities. Commercial kits for soil or feces are often adopted for studies of activated sludge because of a lack of specific kits, but they have never been evaluated regarding their effectiveness and potential biases based on high throughput sequencing. In this study, seven common DNA extraction kits were evaluated, based on not only yield/purity but also sequencing results, using two activated sludge samples (two sub-samples each, i.e. ethanol-fixed and fresh, as-is). The results indicate that the bead-beating step is necessary for DNA extraction from activated sludge. The two kits without the bead-beating step yielded very low amounts of DNA, and the least abundant operational taxonomic units (OTUs), and significantly underestimated the Gram-positive Actinobacteria, Nitrospirae, Chloroflexi, and Alphaproteobacteria and overestimated Gammaproteobacteria, Deltaproteobacteria, Bacteroidetes, and the rare phyla whose cell walls might have been readily broken. Among the other five kits, FastDNA(@) SPIN Kit for Soil extracted the most and the purest DNA. Although the number of total OTUs obtained using this kit was not the highest, the abundant OTUs and abundance of Actinobacteria demonstrated its efficiency. The three MoBio kits and one ZR kit produced fair results, but had a relatively low DNA yield and/or less Actinobacteria-related sequences. Moreover, the 50 % ethanol fixation increased the DNA yield, but did not change the sequenced microbial community in a significant way. Based on the present study, the FastDNA SPIN kit for Soil is recommended for DNA extraction of activated sludge samples. More importantly, the selection of the DNA extraction kit must be done carefully if the samples contain dominant lysing-resistant groups, such as Actinobacteria and Nitrospirae.

  3. The persistent sampling bias in developmental psychology: A call to action.

    PubMed

    Nielsen, Mark; Haun, Daniel; Kärtner, Joscha; Legare, Cristine H

    2017-10-01

    Psychology must confront the bias in its broad literature toward the study of participants developing in environments unrepresentative of the vast majority of the world's population. Here, we focus on the implications of addressing this challenge, highlight the need to address overreliance on a narrow participant pool, and emphasize the value and necessity of conducting research with diverse populations. We show that high-impact-factor developmental journals are heavily skewed toward publishing articles with data from WEIRD (Western, educated, industrialized, rich, and democratic) populations. Most critically, despite calls for change and supposed widespread awareness of this problem, there is a habitual dependence on convenience sampling and little evidence that the discipline is making any meaningful movement toward drawing from diverse samples. Failure to confront the possibility that culturally specific findings are being misattributed as universal traits has broad implications for the construction of scientifically defensible theories and for the reliable public dissemination of study findings. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Jackknife Estimation of Sampling Variance of Ratio Estimators in Complex Samples: Bias and the Coefficient of Variation. Research Report. ETS RR-06-19

    ERIC Educational Resources Information Center

    Oranje, Andreas

    2006-01-01

    A multitude of methods has been proposed to estimate the sampling variance of ratio estimates in complex samples (Wolter, 1985). Hansen and Tepping (1985) studied some of those variance estimators and found that a high coefficient of variation (CV) of the denominator of a ratio estimate is indicative of a biased estimate of the standard error of a…

  5. Exponentially Biased Ground-State Sampling of Quantum Annealing Machines with Transverse-Field Driving Hamiltonians

    NASA Astrophysics Data System (ADS)

    Mandrà, Salvatore; Zhu, Zheng; Katzgraber, Helmut G.

    2017-02-01

    We study the performance of the D-Wave 2X quantum annealing machine on systems with well-controlled ground-state degeneracy. While obtaining the ground state of a spin-glass benchmark instance represents a difficult task, the gold standard for any optimization algorithm or machine is to sample all solutions that minimize the Hamiltonian with more or less equal probability. Our results show that while naive transverse-field quantum annealing on the D-Wave 2X device can find the ground-state energy of the problems, it is not well suited in identifying all degenerate ground-state configurations associated with a particular instance. Even worse, some states are exponentially suppressed, in agreement with previous studies on toy model problems [New J. Phys. 11, 073021 (2009), 10.1088/1367-2630/11/7/073021]. These results suggest that more complex driving Hamiltonians are needed in future quantum annealing machines to ensure a fair sampling of the ground-state manifold.

  6. Exponentially Biased Ground-State Sampling of Quantum Annealing Machines with Transverse-Field Driving Hamiltonians.

    PubMed

    Mandrà, Salvatore; Zhu, Zheng; Katzgraber, Helmut G

    2017-02-17

    We study the performance of the D-Wave 2X quantum annealing machine on systems with well-controlled ground-state degeneracy. While obtaining the ground state of a spin-glass benchmark instance represents a difficult task, the gold standard for any optimization algorithm or machine is to sample all solutions that minimize the Hamiltonian with more or less equal probability. Our results show that while naive transverse-field quantum annealing on the D-Wave 2X device can find the ground-state energy of the problems, it is not well suited in identifying all degenerate ground-state configurations associated with a particular instance. Even worse, some states are exponentially suppressed, in agreement with previous studies on toy model problems [New J. Phys. 11, 073021 (2009)NJOPFM1367-263010.1088/1367-2630/11/7/073021]. These results suggest that more complex driving Hamiltonians are needed in future quantum annealing machines to ensure a fair sampling of the ground-state manifold.

  7. Reactivity-worth estimates of the OSMOSE samples in the MINERVE reactor R1-UO2 configuration.

    SciTech Connect

    Klann, R. T.; Perret, G.; Nuclear Engineering Division

    2007-10-03

    An initial series of calculations of the reactivity-worth of the OSMOSE samples in the MINERVE reactor with the R1-UO2 core configuration were completed. The reactor model was generated using the REBUS code developed at Argonne National Laboratory. The calculations are based on the specifications for fabrication, so they are considered preliminary until sampling and analysis have been completed on the fabricated samples. The estimates indicate a range of reactivity effect from -22 pcm to +25 pcm compared to the natural U sample.

  8. A "Scientific Diversity" Intervention to Reduce Gender Bias in a Sample of Life Scientists

    ERIC Educational Resources Information Center

    Moss-Racusin, Corinne A.; van der Toorn, Jojanneke; Dovidio, John F.; Brescoll, Victoria L.; Graham, Mark J.; Handelsman, Jo

    2016-01-01

    Mounting experimental evidence suggests that subtle gender biases favoring men contribute to the underrepresentation of women in science, technology, engineering, and mathematics (STEM), including many subfields of the life sciences. However, there are relatively few evaluations of diversity interventions designed to reduce gender biases within…

  9. A "Scientific Diversity" Intervention to Reduce Gender Bias in a Sample of Life Scientists

    ERIC Educational Resources Information Center

    Moss-Racusin, Corinne A.; van der Toorn, Jojanneke; Dovidio, John F.; Brescoll, Victoria L.; Graham, Mark J.; Handelsman, Jo

    2016-01-01

    Mounting experimental evidence suggests that subtle gender biases favoring men contribute to the underrepresentation of women in science, technology, engineering, and mathematics (STEM), including many subfields of the life sciences. However, there are relatively few evaluations of diversity interventions designed to reduce gender biases within…

  10. An investigation of arc discharging on negatively biased dielectric conductor samples in a plasma

    NASA Technical Reports Server (NTRS)

    Miller, W. L.

    1985-01-01

    Proposals are now being developed for the construction of high-power photovoltaic systems for operation in low Earth orbit, where the plasma number density is about 1,000 to 1,000,000 per cubic cm. Existing data indicate that interactions between the plasma and high-voltage surfaces of an orbiting power system will occur. In ground tests, where the applied voltage is increased negatively from ground, the array current collection shows an approximately linear rise until it terminates in arcing at greater than several hundred volts negative. This arcing may reduce the power generation efficiency and could possibly affect the low-level logic circuits of the spacecraft. Therefore it is important that the arcing phenomenon be well understood. This study is a survey of the behavior of different dielectric-conductor samples, including a solar cell module, that were biased negatively in a low-density plasma environment with the intent of defining arc discharge conditions and characteristics. Procedures and results are discussed.

  11. Effect of length biased sampling of unobserved sojourn times on the survival distribution when disease is screen detected.

    PubMed

    Kafadar, Karen; Prorok, Philip C

    2009-07-20

    Data can arise as a length-biased sample rather than as a random sample; e.g. a sample of patients in hospitals or of network cable lines (experimental units with longer stays or longer lines have greater likelihoods of being sampled). The distribution arising from a single length-biased sampling (LBS) time has been derived (e.g. (The Statistical Analysis of Discrete Time Events. Oxford Press: London, 1972)) and applies when the observed outcome relates to the random variable subjected to LBS. Zelen (Breast Cancer: Trends in Research and Treatment. Raven Press: New York, 1976; 287-301) noted that cases of disease detected from a screening program likewise form a length-biased sample among all cases, since longer sojourn times afford greater likelihoods of being screen detected. In contrast to the samples on hospital stays and cable lines, however, the length-biased sojourns (preclinical durations) cannot be observed, although their subsequent clinical durations (survival times) are. This article quantifies the effect of LBS of the sojourn times (or pre-clinical durations) on the distribution of the observed clinical durations when cases undergo periodic screening for the early detection of disease. We show that, when preclinical and clinical durations are positively correlated, the mean, median, and quartiles of the distribution of the clinical duration from screen-detected cases can be substantially inflated-even in the absence of any benefit on survival from the screening procedure. Screening studies that report mean survival time need to take account of the fact that, even in the absence of any real benefit, the mean survival among cases in the screen-detected group will be longer than that among interval cases or among cases that arise in the control arm, above and beyond lead time bias, simply by virtue of the LBS phenomenon

  12. Personality Factors and Depressive Configurations. An Exploratory Study in an Italian Clinical Sample

    PubMed Central

    Straccamore, Francesca; Ruggi, Simona; Lingiardi, Vittorio; Zanardi, Raffaella; Vecchi, Sara; Oasi, Osmano

    2017-01-01

    Introduction: This study focuses on the relationship between personality configurations and depressive experiences. More specifically, the aim of this study is to investigate the relationship between self-criticism and dependency and personality styles or disorders, exploring the association between personality features and depressive symptoms. The two-configurations model of personality developed by Blatt (2004, 2008) is adopted as a reference point in sharing a valid framework and in understanding the results. Methods: Five instruments are administered to 51 participants with a diagnosis of depressive disorder, in accordance with DSM-IV-TR (American Psychiatric Association, 2000): Self-criticism and dependency dimensions of depression are measured with the Depressive Experiences Questionnaire (DEQ); self-reported depression is assessed with the Beck Depression Inventory-II (BDI-II); observer-rated depression is assessed with the Hamilton Depression Rating Scale (HDRS); personality is assessed with the Clinical Diagnostic Interview (CDI) and the Shedler Westen Assessment Procedure-200 (SWAP-200). Results: Only self-criticism, and not dependency, is associated with depressive symptoms. In addition, the SWAP Borderline PD Scale and the Dysphoric: Emotionally dysregulated Q-factor emerge as significant in predicting depression. Conclusions: Findings support the assumption that depressive personality configurations can enhance the vulnerability to developing depression. Theoretical and clinical implications of these results are discussed. PMID:28316575

  13. Sources and magnitude of bias associated with determination of polychlorinated biphenyls in environmental samples

    USGS Publications Warehouse

    Eganhouse, R.P.; Gossett, R.W.

    1991-01-01

    Recently complled data on the composition of commercial Aroclor mixtures and ECD (electron capture detector) response factors for all 209 PCB congeners are used to develop estimates of the bias associated with determination of polychlorinated blphenyis. During quantitation of multlcomponent peaks by congener-specific procedures error is introduced because of variable ECD response to isomeric PCBs. Under worst case conditions, the magnitude of this bias can range from less than 2% to as much as 600%. Multicomponent peaks containing the more highly and the lower chlorinated congeners experience the most bias. For this reason, quantitation of ??PCB in Aroclor mixtures dominated by these species (e.g. 1016) are potentially subject to the greatest error. Comparison of response factor data for ECDs from two laboratories shows that the sign and magnitude of calibration bias for a given multicomponent peak is variable and depends, in part, on the response characteristics of individual detectors. By using the most abundant congener (of each multicomponent peak) for purposes of calibration, one can reduce the maximum bias to less than 55%. Moreover, due to cancellation of errors, the bias resulting from summation of all peak concentrations (i.e. ??PCB) becomes vanishingly small (200%) and highly variable in sign and magnitude. In this case, bias originates not only from the incomplete chromatographic resolution of PCB congeners but also the overlapping patterns of the Aroclor mixtures. Together these results illustrate the advantages of the congener-specific method of PCB quantitation over the traditional Aroclor Method and the extreme difficulty of estimating bias incurred by the latter procedure on a post hoc basis.

  14. Addressing small sample size bias in multiple-biomarker trials: Inclusion of biomarker-negative patients and Firth correction.

    PubMed

    Habermehl, Christina; Benner, Axel; Kopp-Schneider, Annette

    2017-08-01

    In recent years, numerous approaches for biomarker-based clinical trials have been developed. One of these developments are multiple-biomarker trials, which aim to investigate multiple biomarkers simultaneously in independent subtrials. For low-prevalence biomarkers, small sample sizes within the subtrials have to be expected, as well as many biomarker-negative patients at the screening stage. The small sample sizes may make it unfeasible to analyze the subtrials individually. This imposes the need to develop new approaches for the analysis of such trials. With an expected large group of biomarker-negative patients, it seems reasonable to explore options to benefit from including them in such trials. We consider advantages and disadvantages of the inclusion of biomarker-negative patients in a multiple-biomarker trial with a survival endpoint. We discuss design options that include biomarker-negative patients in the study and address the issue of small sample size bias in such trials. We carry out a simulation study for a design where biomarker-negative patients are kept in the study and are treated with standard of care. We compare three different analysis approaches based on the Cox model to examine if the inclusion of biomarker-negative patients can provide a benefit with respect to bias and variance of the treatment effect estimates. We apply the Firth correction to reduce the small sample size bias. The results of the simulation study suggest that for small sample situations, the Firth correction should be applied to adjust for the small sample size bias. Additional to the Firth penalty, the inclusion of biomarker-negative patients in the analysis can lead to further but small improvements in bias and standard deviation of the estimates. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. The CO5 configuration of the 7 km Atlantic Margin Model: large-scale biases and sensitivity to forcing, physics options and vertical resolution

    NASA Astrophysics Data System (ADS)

    O'Dea, Enda; Furner, Rachel; Wakelin, Sarah; Siddorn, John; While, James; Sykes, Peter; King, Robert; Holt, Jason; Hewitt, Helene

    2017-08-01

    We describe the physical model component of the standard Coastal Ocean version 5 configuration (CO5) of the European north-west shelf (NWS). CO5 was developed jointly between the Met Office and the National Oceanography Centre. CO5 is designed with the seamless approach in mind, which allows for modelling of multiple timescales for a variety of applications from short-range ocean forecasting to climate projections. The configuration constitutes the basis of the latest update to the ocean and data assimilation components of the Met Office's operational Forecast Ocean Assimilation Model (FOAM) for the NWS. A 30.5-year non-assimilating control hindcast of CO5 was integrated from January 1981 to June 2012. Sensitivity simulations were conducted with reference to the control run. The control run is compared against a previous non-assimilating Proudman Oceanographic Laboratory Coastal Ocean Modelling System (POLCOMS) hindcast of the NWS. The CO5 control hindcast is shown to have much reduced biases compared to POLCOMS. Emphasis in the system description is weighted to updates in CO5 over previous versions. Updates include an increase in vertical resolution, a new vertical coordinate stretching function, the replacement of climatological riverine sources with the pan-European hydrological model E-HYPE, a new Baltic boundary condition and switching from directly imposed atmospheric model boundary fluxes to calculating the fluxes within the model using a bulk formula. Sensitivity tests of the updates are detailed with a view toward attributing observed changes in the new system from the previous system and suggesting future directions of research to further improve the system.

  16. Assessing Intellectual Ability with a Minimum of Cultural Bias for Two Samples of Metis and Indian Children.

    ERIC Educational Resources Information Center

    West, Lloyd Wilbert

    An investigation was designed to ascertain the effects of cultural background on selected intelligence tests and to identify instruments which validly measure intellectual ability with a minimum of cultural bias. A battery of tests, selected for factor analytic study, was administered and replicated at four grade levels to a sample of Metis and…

  17. Assessing Intellectual Ability with a Minimum of Cultural Bias for Two Samples of Metis and Indian Children.

    ERIC Educational Resources Information Center

    West, Lloyd Wilbert

    An investigation was designed to ascertain the effects of cultural background on selected intelligence tests and to identify instruments which validly measure intellectual ability with a minimum of cultural bias. A battery of tests, selected for factor analytic study, was administered and replicated at four grade levels to a sample of Metis and…

  18. Enhanced Conformational Sampling Using Replica Exchange with Concurrent Solute Scaling and Hamiltonian Biasing Realized in One Dimension

    PubMed Central

    2015-01-01

    Replica exchange (REX) is a powerful computational tool for overcoming the quasi-ergodic sampling problem of complex molecular systems. Recently, several multidimensional extensions of this method have been developed to realize exchanges in both temperature and biasing potential space or the use of multiple biasing potentials to improve sampling efficiency. However, increased computational cost due to the multidimensionality of exchanges becomes challenging for use on complex systems under explicit solvent conditions. In this study, we develop a one-dimensional (1D) REX algorithm to concurrently combine the advantages of overall enhanced sampling from Hamiltonian solute scaling and the specific enhancement of collective variables using Hamiltonian biasing potentials. In the present Hamiltonian replica exchange method, termed HREST-BP, Hamiltonian solute scaling is applied to the solute subsystem, and its interactions with the environment to enhance overall conformational transitions and biasing potentials are added along selected collective variables associated with specific conformational transitions, thereby balancing the sampling of different hierarchical degrees of freedom. The two enhanced sampling approaches are implemented concurrently allowing for the use of a small number of replicas (e.g., 6 to 8) in 1D, thus greatly reducing the computational cost in complex system simulations. The present method is applied to conformational sampling of two nitrogen-linked glycans (N-glycans) found on the HIV gp120 envelope protein. Considering the general importance of the conformational sampling problem, HREST-BP represents an efficient procedure for the study of complex saccharides, and, more generally, the method is anticipated to be of general utility for the conformational sampling in a wide range of macromolecular systems. PMID:26082676

  19. Evaluation of ACCMIP ozone simulations and ozonesonde sampling biases using a satellite-based multi-constituent chemical reanalysis

    NASA Astrophysics Data System (ADS)

    Miyazaki, Kazuyuki; Bowman, Kevin

    2017-07-01

    The Atmospheric Chemistry Climate Model Intercomparison Project (ACCMIP) ensemble ozone simulations for the present day from the 2000 decade simulation results are evaluated by a state-of-the-art multi-constituent atmospheric chemical reanalysis that ingests multiple satellite data including the Tropospheric Emission Spectrometer (TES), the Microwave Limb Sounder (MLS), the Ozone Monitoring Instrument (OMI), and the Measurement of Pollution in the Troposphere (MOPITT) for 2005-2009. Validation of the chemical reanalysis against global ozonesondes shows good agreement throughout the free troposphere and lower stratosphere for both seasonal and year-to-year variations, with an annual mean bias of less than 0.9 ppb in the middle and upper troposphere at the tropics and mid-latitudes. The reanalysis provides comprehensive spatiotemporal evaluation of chemistry-model performance that compliments direct ozonesonde comparisons, which are shown to suffer from significant sampling bias. The reanalysis reveals that the ACCMIP ensemble mean overestimates ozone in the northern extratropics by 6-11 ppb while underestimating by up to 18 ppb in the southern tropics over the Atlantic in the lower troposphere. Most models underestimate the spatial variability of the annual mean lower tropospheric concentrations in the extratropics of both hemispheres by up to 70 %. The ensemble mean also overestimates the seasonal amplitude by 25-70 % in the northern extratropics and overestimates the inter-hemispheric gradient by about 30 % in the lower and middle troposphere. A part of the discrepancies can be attributed to the 5-year reanalysis data for the decadal model simulations. However, these differences are less evident with the current sonde network. To estimate ozonesonde sampling biases, we computed model bias separately for global coverage and the ozonesonde network. The ozonesonde sampling bias in the evaluated model bias for the seasonal mean concentration relative to global

  20. The Nonlinear Biasing of the zCOSMOS Galaxies up to z ~ 1 from the 10k Sample

    NASA Astrophysics Data System (ADS)

    Kovač, K.; Porciani, C.; Lilly, S. J.; Marinoni, C.; Guzzo, L.; Cucciati, O.; Zamorani, G.; Iovino, A.; Oesch, P.; Bolzonella, M.; Peng, Y.; Meneux, B.; Zucca, E.; Bardelli, S.; Carollo, C. M.; Contini, T.; Kneib, J.-P.; Le Fèvre, O.; Mainieri, V.; Renzini, A.; Scodeggio, M.; Bongiorno, A.; Caputi, K.; Coppa, G.; de la Torre, S.; de Ravel, L.; Finoguenov, A.; Franzetti, P.; Garilli, B.; Kampczyk, P.; Knobel, C.; Lamareille, F.; Le Borgne, J.-F.; Le Brun, V.; Maier, C.; Mignoli, M.; Pello, R.; Perez-Montero, E.; Pozzetti, L.; Ricciardelli, E.; Silverman, J. D.; Tanaka, M.; Tasca, L. A. M.; Tresse, L.; Vergani, D.; Abbas, U.; Bottini, D.; Cappi, A.; Cassata, P.; Cimatti, A.; Fumana, M.; Koekemoer, A. M.; Leauthaud, A.; Maccagni, D.; McCracken, H. J.; Memeo, P.; Scaramella, R.; Scoville, N. Z.

    2011-04-01

    We use the zCOSMOS galaxy overdensity field to study the biasing of galaxies in the COSMOS field. By comparing the probability distribution function of the galaxy density contrast δ g to the lognormal approximation of the mass density contrast δ, we obtain the mean biasing function b(δ, z, R) between the galaxy and matter overdensity fields and its second moments \\hat{b} and \\tilde{b}. Over the redshift interval 0.4 < z < 1 the conditional mean function langδ g |δrang = b(δ, z, R)δ is of a characteristic shape, requiring nonlinear biasing in the most overdense and underdense regions. Taking into account the uncertainties due to cosmic variance, we do not detect any significant evolution in the langδ g |δrang function, but we do detect a significant redshift evolution in the linear biasing parameter \\hat{b} from 1.23 ± 0.11 at z ~ 0.55 to 1.62 ± 0.14 at z ~ 0.75, for a luminosity-complete sample of MB < -20 - z galaxies. The \\hat{b} parameter does not change significantly with smoothing scale between 8 and 12 h -1 Mpc, but increases systematically with luminosity (at 2σ-3σ significance between the MB < -20.5 - z and MB < -20 - z samples). The nonlinearity parameter \\tilde{b}/ \\hat{b} is offset from unity by at most 2%, with an uncertainty of the same order. The \\tilde{b}/\\hat{b} parameter does not show any significant redshift evolution, dependence on the smoothing scale or on the luminosity. By matching the linear bias of galaxies to the halo bias, we infer that the MB < -20 - z galaxies reside in dark matter halos with a characteristic mass of about (2.6 - 5.6) × 1012 M sun with a small dependence on the adopted bias-mass relation. Our detailed error analysis and comparison with previous studies lead us to conclude that cosmic variance is the main contributor to the differences in the linear bias measured from different surveys. While our results support the general picture of biased galaxy formation up to z ~ 1, the fine-tuning of the galaxy

  1. A two-phase sampling survey for nonresponse and its paradata to correct nonresponse bias in a health surveillance survey.

    PubMed

    Santin, G; Bénézet, L; Geoffroy-Perez, B; Bouyer, J; Guéguen, A

    2017-02-01

    The decline in participation rates in surveys, including epidemiological surveillance surveys, has become a real concern since it may increase nonresponse bias. The aim of this study is to estimate the contribution of a complementary survey among a subsample of nonrespondents, and the additional contribution of paradata in correcting for nonresponse bias in an occupational health surveillance survey. In 2010, 10,000 workers were randomly selected and sent a postal questionnaire. Sociodemographic data were available for the whole sample. After data collection of the questionnaires, a complementary survey among a random subsample of 500 nonrespondents was performed using a questionnaire administered by an interviewer. Paradata were collected for the complete subsample of the complementary survey. Nonresponse bias in the initial sample and in the combined samples were assessed using variables from administrative databases available for the whole sample, not subject to differential measurement errors. Corrected prevalences by reweighting technique were estimated by first using the initial survey alone and then the initial and complementary surveys combined, under several assumptions regarding the missing data process. Results were compared by computing relative errors. The response rates of the initial and complementary surveys were 23.6% and 62.6%, respectively. For the initial and the combined surveys, the relative errors decreased after correction for nonresponse on sociodemographic variables. For the combined surveys without paradata, relative errors decreased compared with the initial survey. The contribution of the paradata was weak. When a complex descriptive survey has a low response rate, a short complementary survey among nonrespondents with a protocol which aims to maximize the response rates, is useful. The contribution of sociodemographic variables in correcting for nonresponse bias is important whereas the additional contribution of paradata in

  2. Quantitative evaluation of bias in PCR amplification and next-generation sequencing derived from metabarcoding samples.

    PubMed

    Pawluczyk, Marta; Weiss, Julia; Links, Matthew G; Egaña Aranguren, Mikel; Wilkinson, Mark D; Egea-Cortines, Marcos

    2015-03-01

    Unbiased identification of organisms by PCR reactions using universal primers followed by DNA sequencing assumes positive amplification. We used six universal loci spanning 48 plant species and quantified the bias at each step of the identification process from end point PCR to next-generation sequencing. End point amplification was significantly different for single loci and between species. Quantitative PCR revealed that Cq threshold for various loci, even within a single DNA extraction, showed 2,000-fold differences in DNA quantity after amplification. Next-generation sequencing (NGS) experiments in nine species showed significant biases towards species and specific loci using adaptor-specific primers. NGS sequencing bias may be predicted to some extent by the Cq values of qPCR amplification.

  3. Atmospheric scanning electron microscope system with an open sample chamber: configuration and applications.

    PubMed

    Nishiyama, Hidetoshi; Koizumi, Mitsuru; Ogawa, Koji; Kitamura, Shinich; Konyuba, Yuji; Watanabe, Yoshiyuki; Ohbayashi, Norihiko; Fukuda, Mitsunori; Suga, Mitsuo; Sato, Chikara

    2014-12-01

    An atmospheric scanning electron microscope (ASEM) with an open sample chamber and optical microscope (OM) is described and recent developments are reported. In this ClairScope system, the base of the open sample dish is sealed to the top of the inverted SEM column, allowing the liquid-immersed sample to be observed by OM from above and by SEM from below. The optical axes of the two microscopes are aligned, ensuring that the same sample areas are imaged to realize quasi-simultaneous correlative microscopy in solution. For example, the cathodoluminescence of ZnO particles was directly demonstrated. The improved system has (i) a fully motorized sample stage, (ii) a column protection system in the case of accidental window breakage, and (iii) an OM/SEM operation system controlled by a graphical user interface. The open sample chamber allows the external administration of reagents during sample observation. We monitored the influence of added NaCl on the random motion of silica particles in liquid. Further, using fluorescence as a transfection marker, the effect of small interfering RNA-mediated knockdown of endogenous Varp on Tyrp1 trafficking in melanocytes was examined. A temperature-regulated titanium ASEM dish allowed the dynamic observation of colloidal silver nanoparticles as they were heated to 240°C and sintered.

  4. The Effects of Sample Selection Bias on Racial Differences in Child Abuse Reporting.

    ERIC Educational Resources Information Center

    Ards, Sheila; Chung, Chanjin; Myers, Samuel L., Jr.

    1998-01-01

    Data from the National Incidence Study (NIS) of Child Abuse and Neglect suggest no racial difference in child maltreatment, although there are more black children within the child welfare population. This study found selection bias in the NIS design caused by the exclusion of family, friends, and neighbors that resulted in differences in NIS cases…

  5. Use of Bayes theorem to correct size-specific sampling bias in growth data.

    PubMed

    Troynikov, V S

    1999-03-01

    The bayesian decomposition of posterior distribution was used to develop a likelihood function to correct bias in the estimates of population parameters from data collected randomly with size-specific selectivity. Positive distributions with time as a parameter were used for parametrization of growth data. Numerical illustrations are provided. The alternative applications of the likelihood to estimate selectivity parameters are discussed.

  6. A Critical Assessment of Bias in Survey Studies Using Location-Based Sampling to Recruit Patrons in Bars

    PubMed Central

    Morrison, Christopher; Lee, Juliet P.; Gruenewald, Paul J.; Marzell, Miesha

    2015-01-01

    Location-based sampling is a method to obtain samples of people within ecological contexts relevant to specific public health outcomes. Random selection increases generalizability, however in some circumstances (such as surveying bar patrons) recruitment conditions increase risks of sample bias. We attempted to recruit representative samples of bars and patrons in six California cities, but low response rates precluded meaningful analysis. A systematic review of 24 similar studies revealed that none addressed the key shortcomings of our study. We recommend steps to improve studies that use location-based sampling: (i) purposively sample places of interest, (ii) utilize recruitment strategies appropriate to the environment, and (iii) provide full information on response rates at all levels of sampling. PMID:26574657

  7. A Critical Assessment of Bias in Survey Studies Using Location-Based Sampling to Recruit Patrons in Bars.

    PubMed

    Morrison, Christopher; Lee, Juliet P; Gruenewald, Paul J; Marzell, Miesha

    2015-01-01

    Location-based sampling is a method to obtain samples of people within ecological contexts relevant to specific public health outcomes. Random selection increases generalizability; however, in some circumstances (such as surveying bar patrons), recruitment conditions increase risks of sample bias. We attempted to recruit representative samples of bars and patrons in six California cities, but low response rates precluded meaningful analysis. A systematic review of 24 similar studies revealed that none addressed the key shortcomings of our study. We recommend steps to improve studies that use location-based sampling: (i) purposively sample places of interest, (ii) use recruitment strategies appropriate to the environment, and (iii) provide full information on response rates at all levels of sampling.

  8. Equal path, phase shifting, sample point interferometer for monitoring the configuration of surfaces

    NASA Technical Reports Server (NTRS)

    Manhart, Paul K. (Inventor)

    1992-01-01

    A system for monitoring the configuration of a surface (e.g., a segmented parabolic surface) using orthogonally placed retroreflectors at sets of points 1, 2, and 3 dispersed throughout the surface with a stationary halfwave plate (HWP) in the front of the one retroreflector at a corner point 3 and a rotating halfwave plate (RHWP) over a source of linearly polarized coherent light, thereby causing the direction of linear polarization to continuously rotate through 360 deg and causing light returned by the retroreflector at point 3 to be continuously phase shifted through 360 deg relative to light returned by retroreflectors at points 1 and 2. The returned light from each set of points 1, 2, and 3 is focused onto a bed-of-nails (BON) phase grating diagonally oriented with respect to the orthogonal orientation of the incident beams from retroreflectors 1, 2, and 3, thereby causing overlap in the light from points 1 and 3 to produce interferometric signals 1,3 and 2,3. Any change in phase of the interferometric signals 1,3 and 2,3 indicates both the magnitude and direction of any change in the position of the retroreflector at point 3 relative to retroreflectors at points 1 and 2.

  9. High-resolution room-temperature sample scanning superconducting quantum interference device microscope configurable for geological and biomagnetic applications

    NASA Astrophysics Data System (ADS)

    Fong, L. E.; Holzer, J. R.; McBride, K. K.; Lima, E. A.; Baudenbacher, F.; Radparvar, M.

    2005-05-01

    We have developed a scanning superconducting quantum interference device (SQUID) microscope system with interchangeable sensor configurations for imaging magnetic fields of room-temperature (RT) samples with submillimeter resolution. The low-critical-temperature (Tc) niobium-based monolithic SQUID sensors are mounted on the tip of a sapphire and thermally anchored to the helium reservoir. A 25μm sapphire window separates the vacuum space from the RT sample. A positioning mechanism allows us to adjust the sample-to-sensor spacing from the top of the Dewar. We achieved a sensor-to-sample spacing of 100μm, which could be maintained for periods of up to four weeks. Different SQUID sensor designs are necessary to achieve the best combination of spatial resolution and field sensitivity for a given source configuration. For imaging thin sections of geological samples, we used a custom-designed monolithic low-Tc niobium bare SQUID sensor, with an effective diameter of 80μm, and achieved a field sensitivity of 1.5pT/Hz1/2 and a magnetic moment sensitivity of 5.4×10-18Am2/Hz1/2 at a sensor-to-sample spacing of 100μm in the white noise region for frequencies above 100Hz. Imaging action currents in cardiac tissue requires a higher field sensitivity, which can only be achieved by compromising spatial resolution. We developed a monolithic low-Tc niobium multiloop SQUID sensor, with sensor sizes ranging from 250μm to 1mm, and achieved sensitivities of 480-180fT /Hz1/2 in the white noise region for frequencies above 100Hz, respectively. For all sensor configurations, the spatial resolution was comparable to the effective diameter and limited by the sensor-to-sample spacing. Spatial registration allowed us to compare high-resolution images of magnetic fields associated with action currents and optical recordings of transmembrane potentials to study the bidomain nature of cardiac tissue or to match petrography to magnetic field maps in thin sections of geological samples.

  10. Screening for psychotic experiences: social desirability biases in a non-clinical sample.

    PubMed

    DeVylder, Jordan E; Hilimire, Matthew R

    2015-08-01

    Subthreshold psychotic experiences are common in the population and may be clinically significant. Reporting of psychotic experiences through self-report screens may be subject to threats to validity, including social desirability biases. This study examines the influence of social desirability on the reporting of psychotic experiences. College students (n = 686) completed a psychosis screen and the Marlowe-Crowne social desirability scale as part of a self-report survey battery. Associations between psychosis and social desirability were tested using logistic regression models. With the exception of auditory hallucinations, all other measures of psychotic experiences were subject to social desirability biases. Respondents who gave more socially desirable answers were less likely to report psychotic experiences. Respondent's tendency to underreport psychotic experiences should be accounted for when screening for these symptoms clinically. Findings also suggest that population figures based on self-report may underestimate the prevalence of subthreshold delusions but not hallucinations. © 2014 Wiley Publishing Asia Pty Ltd.

  11. The effect of sample size and bias on the reliability of estimates of error: a comparative study of Dahlberg's formula.

    PubMed

    Springate, S D

    2012-04-01

    This study examined the effects of different sample sizes and different levels of bias (systematic error) between replicated measurements on the accuracy of estimates of random error calculated using two common formulae: Dahlberg's and the 'method of moments' estimator (MME). Computer-based numerical simulations were used to generate clinically realistic measurements involving random errors with a known distribution. For each simulation, two sets of 'measured values' were generated to provide the replicated data necessary for the estimation of the random error. Dahlberg's and the MME formula were applied to these paired data sets and the resulting estimates of error compared with the 'true' error. Nine different sample sizes (n = 2, 5, 10, 15, 20, 25, 30, 50, and 100) and two different types of bias (additive and multiplicative) were examined for their effect on the estimated error. In each case, the estimates of the random error were based on the distribution of 5000 separate simulations. The results indicate that with a sample of less than 25-30 replicated measurements, the resulting estimates of error are potentially unreliable and may under or overestimate the true error, irrespective of the formula used in the calculation. Where, however, a bias exists between the replicate measurements, Dahlberg's formula can be expected to overestimate the true value of the random error even where the biases are small and difficult to detect by standard statistical tests. No such distorting effect was found for the MME formula, which provided estimates of error that were not meaningfully different from the true value even where relatively large biases existed between the replicates. These results suggest the following: 1. A sample of at least 25-30 cases should be replicated to provide an estimate of the random error. 2. Where the original study contains fewer than 20 cases, the estimate of error will be unreliable. In these circumstances, it would be helpful if a confidence

  12. Effectiveness comparison of multiple sticky-trap configurations for sampling Pseudacteon spp. phorid flies (Diptera: Phoridae).

    PubMed

    Puckett, R T; Calixto, A A; Reed, J J; McDonald, D L; Drees, B Bart; Gold, R E

    2013-08-01

    A variety of traps have been developed for monitoring introduced populations of Pseudacteon spp. phorid flies (Diptera: Phoridae) across their established range in the United States. Such traps typically exploit common aspects of phorid fly biology and behavior, such as their attraction to live or dead red imported fire ants, Solenopsis invicta Buren (Hymenoptera: Formicidae), as well as the perching behavior of these parasitoids. However, populations of multiple species of phorid flies have been established in the United States to serve as biological control agents against S. invicta, and it is unclear if all trap designs are equally effective in sampling this variety of phorid species. This study investigated the effectiveness of six trap designs simultaneously during three sampling events in south-central Texas. Interactions between two species of phorid flies (Pseudacteon tricuspis Borgmeier and P. curvatus B.) and their hosts have been intensively studied at this location for over eight years. When analyzed independently, there were no significant differences in the mean number of P. curvatus or P. tricuspis phorids collected by any of the trap designs during any of the sampling events. However, when the total number of phorids collected were combined, significant trap performance differentials were observed during the October 2010 sampling event. Furthermore, there were significant differences among male flies during the September 2012 observation. Additionally, a trap component cost comparison is provided. The consistent and relatively equivalent performance of the phorid traps investigated in these trials suggests that all are appropriate for phorid surveillance, and cost and ease-of-use considerations may be the most important criteria when selecting a trap design.

  13. MaxEnt's parameter configuration and small samples: are we paying attention to recommendations? A systematic review.

    PubMed

    Morales, Narkis S; Fernández, Ignacio C; Baca-González, Victoria

    2017-01-01

    Environmental niche modeling (ENM) is commonly used to develop probabilistic maps of species distribution. Among available ENM techniques, MaxEnt has become one of the most popular tools for modeling species distribution, with hundreds of peer-reviewed articles published each year. MaxEnt's popularity is mainly due to the use of a graphical interface and automatic parameter configuration capabilities. However, recent studies have shown that using the default automatic configuration may not be always appropriate because it can produce non-optimal models; particularly when dealing with a small number of species presence points. Thus, the recommendation is to evaluate the best potential combination of parameters (feature classes and regularization multiplier) to select the most appropriate model. In this work we reviewed 244 articles published between 2013 and 2015 to assess whether researchers are following recommendations to avoid using the default parameter configuration when dealing with small sample sizes, or if they are using MaxEnt as a "black box tool." Our results show that in only 16% of analyzed articles authors evaluated best feature classes, in 6.9% evaluated best regularization multipliers, and in a meager 3.7% evaluated simultaneously both parameters before producing the definitive distribution model. We analyzed 20 articles to quantify the potential differences in resulting outputs when using software default parameters instead of the alternative best model. Results from our analysis reveal important differences between the use of default parameters and the best model approach, especially in the total area identified as suitable for the assessed species and the specific areas that are identified as suitable by both modelling approaches. These results are worrying, because publications are potentially reporting over-complex or over-simplistic models that can undermine the applicability of their results. Of particular importance are studies used to

  14. Testing Large CICC in Short Sample Configuration and Predicting Their Performance in Large Magnets

    SciTech Connect

    Martovetsky, N N

    2007-08-24

    It is well known that large Nb3Sn Cable-in-Conduit Conductors (CICC) do not always completely utilize current carrying capacity of the strands they are made of. The modern state of theory is not accurate enough to eliminate CICC full scale testing. Measuring properties of large CICC is not a simple task due to variety of parameters that need to be controlled, like temperature, exposure of all the strands to the peak magnetic field, mass flow and particular nonuniform current distribution. The paper presents some measurement issues of CICC testing in a short sample test facility, particularly, conditions for uniform current distribution and effect of twist pitches on the critical current.

  15. On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations

    PubMed Central

    2011-01-01

    We have implemented the accelerated molecular dynamics approach (Hamelberg, D.; Mongan, J.; McCammon, J. A. J. Chem. Phys. 2004, 120 (24), 11919) in the framework of ab initio MD (AIMD). Using three simple examples, we demonstrate that accelerated AIMD (A-AIMD) can be used to accelerate solvent relaxation in AIMD simulations and facilitate the detection of reaction coordinates: (i) We show, for one cyclohexane molecule in the gas phase, that the method can be used to accelerate the rate of the chair-to-chair interconversion by a factor of ∼1 × 105, while allowing for the reconstruction of the correct canonical distribution of low-energy states; (ii) We then show, for a water box of 64 H2O molecules, that A-AIMD can also be used in the condensed phase to accelerate the sampling of water conformations, without affecting the structural properties of the solvent; and (iii) The method is then used to compute the potential of mean force (PMF) for the dissociation of Na−Cl in water, accelerating the convergence by a factor of ∼3−4 compared to conventional AIMD simulations.(2) These results suggest that A-AIMD is a useful addition to existing methods for enhanced conformational and phase-space sampling in solution. While the method does not make the use of collective variables superfluous, it also does not require the user to define a set of collective variables that can capture all the low-energy minima on the potential energy surface. This property may prove very useful when dealing with highly complex multidimensional systems that require a quantum mechanical treatment. PMID:21494425

  16. Sampling ARG of multiple populations under complex configurations of subdivision and admixture.

    PubMed

    Carrieri, Anna Paola; Utro, Filippo; Parida, Laxmi

    2016-04-01

    Simulating complex evolution scenarios of multiple populations is an important task for answering many basic questions relating to population genomics. Apart from the population samples, the underlying Ancestral Recombinations Graph (ARG) is an additional important means in hypothesis checking and reconstruction studies. Furthermore, complex simulations require a plethora of interdependent parameters making even the scenario-specification highly non-trivial. We present an algorithm SimRA that simulates generic multiple population evolution model with admixture. It is based on random graphs that improve dramatically in time and space requirements of the classical algorithm of single populations.Using the underlying random graphs model, we also derive closed forms of expected values of the ARG characteristics i.e., height of the graph, number of recombinations, number of mutations and population diversity in terms of its defining parameters. This is crucial in aiding the user to specify meaningful parameters for the complex scenario simulations, not through trial-and-error based on raw compute power but intelligent parameter estimation. To the best of our knowledge this is the first time closed form expressions have been computed for the ARG properties. We show that the expected values closely match the empirical values through simulations.Finally, we demonstrate that SimRA produces the ARG in compact forms without compromising any accuracy. We demonstrate the compactness and accuracy through extensive experiments. SimRA (Simulation based on Random graph Algorithms) source, executable, user manual and sample input-output sets are available for downloading at: https://github.com/ComputationalGenomics/SimRA CONTACT: : parida@us.ibm.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  17. Clinical Correlates of the Weight Bias Internalization Scale in a Sample of Obese Adolescents Seeking Bariatric Surgery

    PubMed Central

    Roberto, Christina A.; Sysko, Robyn; Bush, Jennifer; Pearl, Rebecca; Puhl, Rebecca M.; Schvey, Natasha A.; Dovidio, John F.

    2012-01-01

    The aim of this study was to evaluate psychometric properties and clinical correlates of the Weight Bias Internalization Scale (WBIS) in a sample of obese adolescents seeking bariatric surgery. Sixty five adolescents enrolled in a bariatric surgery program at a large, urban medical center completed psychiatric evaluations, self-report questionnaires including the WBIS and other measures of psychopathology and physical assessments. The WBIS had high internal consistency (Cronbach’s α = .92). As in previous research with adults, the one underlying factor structure was replicated and 10 of the original 11 items were retained. The scale had significant partial correlations with depression (r = .519), anxiety (r = .465), social and behavioral problems (r = .364), quality of life (r = −.480), and eating (r = .579), shape (r = .815), and weight concerns (r = .545), controlling for body mass index. However, WBIS scores did not predict current or past psychiatric diagnosis or treatment or past suicidal ideation. Overall, the WBIS had excellent psychometric properties in a sample of obese treatment-seeking adolescents and correlated significantly with levels of psychopathology. These findings suggest that the WBIS could be a useful tool for healthcare providers to assess internalized weight bias among treatment-seeking obese youth. Assessment of internalized weight bias among this clinical population has the potential to identify adolescents who may benefit from information on coping with weight stigma which in turn can augment weight loss efforts. PMID:21593805

  18. Sampling biases in datasets of historical mean air temperature over land.

    PubMed

    Wang, Kaicun

    2014-04-10

    Global mean surface air temperature (Ta) has been reported to have risen by 0.74°C over the last 100 years. However, the definition of mean Ta is still a subject of debate. The most defensible definition might be the integral of the continuous temperature measurements over a day (Td0). However, for technological and historical reasons, mean Ta over land have been taken to be the average of the daily maximum and minimum temperature measurements (Td1). All existing principal global temperature analyses over land rely heavily on Td1. Here, I make a first quantitative assessment of the bias in the use of Td1 to estimate trends of mean Ta using hourly Ta observations at 5600 globally distributed weather stations from the 1970s to 2013. I find that the use of Td1 has a negligible impact on the global mean warming rate. However, the trend of Td1 has a substantial bias at regional and local scales, with a root mean square error of over 25% at 5° × 5° grids. Therefore, caution should be taken when using mean Ta datasets based on Td1 to examine high resolution details of warming trends.

  19. Sampling Biases in Datasets of Historical Mean Air Temperature over Land

    NASA Astrophysics Data System (ADS)

    Wang, Kaicun

    2014-04-01

    Global mean surface air temperature (Ta) has been reported to have risen by 0.74°C over the last 100 years. However, the definition of mean Ta is still a subject of debate. The most defensible definition might be the integral of the continuous temperature measurements over a day (Td0). However, for technological and historical reasons, mean Ta over land have been taken to be the average of the daily maximum and minimum temperature measurements (Td1). All existing principal global temperature analyses over land rely heavily on Td1. Here, I make a first quantitative assessment of the bias in the use of Td1 to estimate trends of mean Ta using hourly Ta observations at 5600 globally distributed weather stations from the 1970s to 2013. I find that the use of Td1 has a negligible impact on the global mean warming rate. However, the trend of Td1 has a substantial bias at regional and local scales, with a root mean square error of over 25% at 5° × 5° grids. Therefore, caution should be taken when using mean Ta datasets based on Td1 to examine high resolution details of warming trends.

  20. Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression.

    PubMed

    Meng, Yilin; Roux, Benoît

    2015-08-11

    The weighted histogram analysis method (WHAM) is a standard protocol for postprocessing the information from biased umbrella sampling simulations to construct the potential of mean force with respect to a set of order parameters. By virtue of the WHAM equations, the unbiased density of state is determined by satisfying a self-consistent condition through an iterative procedure. While the method works very effectively when the number of order parameters is small, its computational cost grows rapidly in higher dimension. Here, we present a simple and efficient alternative strategy, which avoids solving the self-consistent WHAM equations iteratively. An efficient multivariate linear regression framework is utilized to link the biased probability densities of individual umbrella windows and yield an unbiased global free energy landscape in the space of order parameters. It is demonstrated with practical examples that free energy landscapes that are comparable in accuracy to WHAM can be generated at a small fraction of the cost.

  1. Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression

    PubMed Central

    2015-01-01

    The weighted histogram analysis method (WHAM) is a standard protocol for postprocessing the information from biased umbrella sampling simulations to construct the potential of mean force with respect to a set of order parameters. By virtue of the WHAM equations, the unbiased density of state is determined by satisfying a self-consistent condition through an iterative procedure. While the method works very effectively when the number of order parameters is small, its computational cost grows rapidly in higher dimension. Here, we present a simple and efficient alternative strategy, which avoids solving the self-consistent WHAM equations iteratively. An efficient multivariate linear regression framework is utilized to link the biased probability densities of individual umbrella windows and yield an unbiased global free energy landscape in the space of order parameters. It is demonstrated with practical examples that free energy landscapes that are comparable in accuracy to WHAM can be generated at a small fraction of the cost. PMID:26574437

  2. Verification of a depth-integrated sample arm as a means to reduce solids stratification bias in urban stormwater sampling.

    PubMed

    Selbig, William R; Cox, Amanda; Bannerman, Roger T

    2012-04-01

    A new water sample collection system was developed to improve representation of solids entrained in urban stormwater by integrating water-quality samples from the entire water column, rather than a single, fixed point. The depth-integrated sample arm (DISA) was better able to characterize suspended-sediment concentration and particle size distribution compared to fixed-point methods when tested in a controlled laboratory environment. Median suspended-sediment concentrations overestimated the actual concentration by 49 and 7% when sampling the water column at 3- and 4-points spaced vertically throughout the water column, respectively. Comparatively, sampling only at the bottom of the pipe, the fixed-point overestimated the actual concentration by 96%. The fixed-point sampler also showed a coarser particle size distribution compared to the DISA which was better able to reproduce the average distribution of particles in the water column over a range of hydraulic conditions. These results emphasize the need for a water sample collection system that integrates the entire water column, rather than a single, fixed point to properly characterize the concentration and distribution of particles entrained in stormwater pipe flow.

  3. Blinded sample size re-estimation in superiority and noninferiority trials: bias versus variance in variance estimation.

    PubMed

    Friede, Tim; Kieser, Meinhard

    2013-01-01

    The internal pilot study design allows for modifying the sample size during an ongoing study based on a blinded estimate of the variance thus maintaining the trial integrity. Various blinded sample size re-estimation procedures have been proposed in the literature. We compare the blinded sample size re-estimation procedures based on the one-sample variance of the pooled data with a blinded procedure using the randomization block information with respect to bias and variance of the variance estimators, and the distribution of the resulting sample sizes, power, and actual type I error rate. For reference, sample size re-estimation based on the unblinded variance is also included in the comparison. It is shown that using an unbiased variance estimator (such as the one using the randomization block information) for sample size re-estimation does not guarantee that the desired power is achieved. Moreover, in situations that are common in clinical trials, the variance estimator that employs the randomization block length shows a higher variability than the simple one-sample estimator and in turn the sample size resulting from the related re-estimation procedure. This higher variability can lead to a lower power as was demonstrated in the setting of noninferiority trials. In summary, the one-sample estimator obtained from the pooled data is extremely simple to apply, shows good performance, and is therefore recommended for application.

  4. Radionuclide Activities in Contaminated Soils: Effects of Sampling Bias on Remediation of Coarse-Grained Soils in Hanford Formation

    SciTech Connect

    Mattigod, Shas V.; Martin, Wayne J.

    2001-08-28

    Only a limited set of particle size-contaminant concentration data is available for soils from the Hanford Site. These data are based on bench-scale tests on single soil samples from one waste site each in operable units 100-BC-1, 100-DR-1, and 100-FR-1, and three samples from the North Pond 300-FF-1 operable unit. The objective of this study was to 1) examine available particle size-contaminant of concern activity and concentration data for 100 and 300 Area soils, 2) assess the effects of sampling bias, 3) suggest sampling protocols, and 4) formulate a method to determine the contaminant of concern activities and concentrations of the whole soil based on the measurements conducted on a finer size fraction of the whole soil.

  5. Given the increasing bias in random digit dial sampling, could respondent-driven sampling be a practical alternative?

    PubMed

    Lee, Robin; Ranaldi, Jennifer; Cummings, Michelle; Crucetti, James B; Stratton, Howard; McNutt, Louise-Anne

    2011-04-01

    Increasing cellular phone service and nonresponse are causing random digit dial (RDD) users to search for alternative ways of sampling geographically large populations. This study evaluated the feasibility and utility in using a modified version of respondent-driven sampling (RDS) as an alternative method. Using RDS, 469 residents of Albany County, New York were enrolled into a telephone-based health survey. Participants answered health and RDS feasibility questions. Results were compared to a previously collected RDD sample and census data. Participation was high (81.4%) and participants referred at least one peer 65.9% of the time. The RDS method produced a more ethnically diverse sample, otherwise respondent demographics were similar to the RDD sample. The most common reason for participating (51.9%) was because a peer told them about the study; 44.9% would not have participated in an RDD study. Persons not willing to participate in a RDD study reported being less healthy and less likely to participate in healthy activities (e.g., have a physical exam in the past 24 months). Although more research is needed, RDS methods may be developed into a viable alternative for collecting health data from large general populations. Copyright © 2011 Elsevier Inc. All rights reserved.

  6. Quantitative Characterization of Configurational Space Sampled by HIV-1 Nucleocapsid Using Solution NMR, X-ray Scattering and Protein Engineering.

    PubMed

    Deshmukh, Lalit; Schwieters, Charles D; Grishaev, Alexander; Clore, G Marius

    2016-06-03

    Nucleic-acid-related events in the HIV-1 replication cycle are mediated by nucleocapsid, a small protein comprising two zinc knuckles connected by a short flexible linker and flanked by disordered termini. Combining experimental NMR residual dipolar couplings, solution X-ray scattering and protein engineering with ensemble simulated annealing, we obtain a quantitative description of the configurational space sampled by the two zinc knuckles, the linker and disordered termini in the absence of nucleic acids. We first compute the conformational ensemble (with an optimal size of three members) of an engineered nucleocapsid construct lacking the N- and C-termini that satisfies the experimental restraints, and then validate this ensemble, as well as characterize the disordered termini, using the experimental data from the full-length nucleocapsid construct. The experimental and computational strategy is generally applicable to multidomain proteins. Differential flexibility within the linker results in asymmetric motion of the zinc knuckles which may explain their functionally distinct roles despite high sequence identity. One of the configurations (populated at a level of ≈40 %) closely resembles that observed in various ligand-bound forms, providing evidence for conformational selection and a mechanistic link between protein dynamics and function. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Development of a depth-integrated sample arm (DISA) to reduce solids stratification bias in stormwater sampling

    USGS Publications Warehouse

    Selbig, William R.; ,; Roger T. Bannerman,

    2011-01-01

    A new depth-integrated sample arm (DISA) was developed to improve the representation of solids in stormwater, both organic and inorganic, by collecting a water quality sample from multiple points in the water column. Data from this study demonstrate the idea of vertical stratification of solids in storm sewer runoff. Concentrations of suspended sediment in runoff were statistically greater using a fixed rather than multipoint collection system. Median suspended sediment concentrations measured at the fixed location (near the pipe invert) were approximately double those collected using the DISA. In general, concentrations and size distributions of suspended sediment decreased with increasing vertical distance from the storm sewer invert. Coarser particles tended to dominate the distribution of solids near the storm sewer invert as discharge increased. In contrast to concentration and particle size, organic material, to some extent, was distributed homogenously throughout the water column, likely the result of its low specific density, which allows for thorough mixing in less turbulent water.

  8. Sample Size Requirements for Structural Equation Models: An Evaluation of Power, Bias, and Solution Propriety

    ERIC Educational Resources Information Center

    Wolf, Erika J.; Harrington, Kelly M.; Clark, Shaunna L.; Miller, Mark W.

    2013-01-01

    Determining sample size requirements for structural equation modeling (SEM) is a challenge often faced by investigators, peer reviewers, and grant writers. Recent years have seen a large increase in SEMs in the behavioral science literature, but consideration of sample size requirements for applied SEMs often relies on outdated rules-of-thumb.…

  9. Sample Size Requirements for Structural Equation Models: An Evaluation of Power, Bias, and Solution Propriety

    ERIC Educational Resources Information Center

    Wolf, Erika J.; Harrington, Kelly M.; Clark, Shaunna L.; Miller, Mark W.

    2013-01-01

    Determining sample size requirements for structural equation modeling (SEM) is a challenge often faced by investigators, peer reviewers, and grant writers. Recent years have seen a large increase in SEMs in the behavioral science literature, but consideration of sample size requirements for applied SEMs often relies on outdated rules-of-thumb.…

  10. Selection bias in dynamically measured supermassive black hole samples: its consequences and the quest for the most fundamental relation

    NASA Astrophysics Data System (ADS)

    Shankar, Francesco; Bernardi, Mariangela; Sheth, Ravi K.; Ferrarese, Laura; Graham, Alister W.; Savorgnan, Giulia; Allevato, Viola; Marconi, Alessandro; Läsker, Ronald; Lapi, Andrea

    2016-08-01

    We compare the set of local galaxies having dynamically measured black holes with a large, unbiased sample of galaxies extracted from the Sloan Digital Sky Survey. We confirm earlier work showing that the majority of black hole hosts have significantly higher velocity dispersions σ than local galaxies of similar stellar mass. We use Monte Carlo simulations to illustrate the effect on black hole scaling relations if this bias arises from the requirement that the black hole sphere of influence must be resolved to measure black hole masses with spatially resolved kinematics. We find that this selection effect artificially increases the normalization of the Mbh-σ relation by a factor of at least ˜3; the bias for the Mbh-Mstar relation is even larger. Our Monte Carlo simulations and analysis of the residuals from scaling relations both indicate that σ is more fundamental than Mstar or effective radius. In particular, the Mbh-Mstar relation is mostly a consequence of the Mbh-σ and σ-Mstar relations, and is heavily biased by up to a factor of 50 at small masses. This helps resolve the discrepancy between dynamically based black hole-galaxy scaling relations versus those of active galaxies. Our simulations also disfavour broad distributions of black hole masses at fixed σ. Correcting for this bias suggests that the calibration factor used to estimate black hole masses in active galaxies should be reduced to values of fvir ˜ 1. Black hole mass densities should also be proportionally smaller, perhaps implying significantly higher radiative efficiencies/black hole spins. Reducing black hole masses also reduces the gravitational wave signal expected from black hole mergers.

  11. A bias against disconfirmatory evidence is associated with delusion proneness in a nonclinical sample.

    PubMed

    Woodward, Todd S; Buchy, Lisa; Moritz, Steffen; Liotti, Mario

    2007-07-01

    Previous work has suggested that a bias against disconfirmatory evidence (BADE) may be associated with the schizophrenia spectrum. The current investigation focused on whether a BADE (1) overlaps with traditional measures of memory and executive functions or selectively taps into a unique aspect of cognition and (2) is correlated with delusional ideation but not with other aspects of schizotypy. Sixty-eight undergraduate students were administered the Schizotypal Personality Questionnaire (SPQ), the BADE test, the Rey Auditory Verbal Learning Test (RAVLT), the Wisconsin Card Sorting Test (WCST), the Trail Making Tests A and B (TMT), and tests used to estimate IQ. Factor analysis of all cognition measures resulted in a 6-factor solution, 4 of which reflected the 4 domains of neuropsychological tests (WCST, RAVLT, TMT, and IQ), and 2 of which reflected different aspects of the BADE test: Initial Belief and Integration of Disconfirmatory Evidence. This solution suggests that BADE measures were independent from the other cognitive domains measured. Integration of Disconfirmatory Evidence was the only factor that correlated with delusion-content subscales of the SPQ, providing support for the contribution of a BADE to delusional ideation.

  12. A Bias Against Disconfirmatory Evidence Is Associated With Delusion Proneness in a Nonclinical Sample

    PubMed Central

    Woodward, Todd S.; Buchy, Lisa; Moritz, Steffen; Liotti, Mario

    2007-01-01

    Previous work has suggested that a bias against disconfirmatory evidence (BADE) may be associated with the schizophrenia spectrum. The current investigation focused on whether a BADE (1) overlaps with traditional measures of memory and executive functions or selectively taps into a unique aspect of cognition and (2) is correlated with delusional ideation but not with other aspects of schizotypy. Sixty-eight undergraduate students were administered the Schizotypal Personality Questionnaire (SPQ), the BADE test, the Rey Auditory Verbal Learning Test (RAVLT), the Wisconsin Card Sorting Test (WCST), the Trail Making Tests A and B (TMT), and tests used to estimate IQ. Factor analysis of all cognition measures resulted in a 6-factor solution, 4 of which reflected the 4 domains of neuropsychological tests (WCST, RAVLT, TMT, and IQ), and 2 of which reflected different aspects of the BADE test: Initial Belief and Integration of Disconfirmatory Evidence. This solution suggests that BADE measures were independent from the other cognitive domains measured. Integration of Disconfirmatory Evidence was the only factor that correlated with delusion-content subscales of the SPQ, providing support for the contribution of a BADE to delusional ideation. PMID:17347526

  13. Sample bias from different recruitment strategies in a randomised controlled trial for alcohol dependence.

    PubMed

    Morley, Kirsten C; Teesson, Maree; Sannibale, Claudia; Haber, Paul S

    2009-05-01

    Participants may be recruited from diverse sources for randomised controlled trials (RCT) of treatments for alcohol dependence. A mixed recruitment strategy might facilitate recruitment and increase generalisability at the expense of introducing systematic selection bias. The current study aims to compare the effects of recruitment method on socio-demographics, baseline illness characteristics, treatment retention and treatment outcome measures. A secondary analysis from a previous 12 week RCT of naltrexone, acamprosate and placebo for alcohol dependence was conducted. Participants (n = 169) were obtained via four channels of recruitment including in-patient and outpatient referral, live media and print media solicitation. Baseline parameters, retention in treatment and treatment outcomes were compared in these groups. Relative to in-patient subjects, those recruited via live and print media had significantly lower scores on taking steps, less in-patient rehabilitation admissions and less previous abstinence before entering the trial. Subjects recruited via print media had significantly lower scores of alcohol dependence relative to all other modes recruitment. There were no differences between recruitment strategies on treatment retention or compliance. At outcome, no significant effect of recruitment method was detected. These results suggest that different recruitment methods may be sourcing subjects with different baseline characteristics of illness. Nonetheless, these differences did not significantly impact on treatment retention or outcome, suggesting that in this population it was appropriate to recruit subjects from mixed sources.

  14. MaxEnt’s parameter configuration and small samples: are we paying attention to recommendations? A systematic review

    PubMed Central

    Baca-González, Victoria

    2017-01-01

    Environmental niche modeling (ENM) is commonly used to develop probabilistic maps of species distribution. Among available ENM techniques, MaxEnt has become one of the most popular tools for modeling species distribution, with hundreds of peer-reviewed articles published each year. MaxEnt’s popularity is mainly due to the use of a graphical interface and automatic parameter configuration capabilities. However, recent studies have shown that using the default automatic configuration may not be always appropriate because it can produce non-optimal models; particularly when dealing with a small number of species presence points. Thus, the recommendation is to evaluate the best potential combination of parameters (feature classes and regularization multiplier) to select the most appropriate model. In this work we reviewed 244 articles published between 2013 and 2015 to assess whether researchers are following recommendations to avoid using the default parameter configuration when dealing with small sample sizes, or if they are using MaxEnt as a “black box tool.” Our results show that in only 16% of analyzed articles authors evaluated best feature classes, in 6.9% evaluated best regularization multipliers, and in a meager 3.7% evaluated simultaneously both parameters before producing the definitive distribution model. We analyzed 20 articles to quantify the potential differences in resulting outputs when using software default parameters instead of the alternative best model. Results from our analysis reveal important differences between the use of default parameters and the best model approach, especially in the total area identified as suitable for the assessed species and the specific areas that are identified as suitable by both modelling approaches. These results are worrying, because publications are potentially reporting over-complex or over-simplistic models that can undermine the applicability of their results. Of particular importance are studies used to

  15. Species-genetic diversity correlations in habitat fragmentation can be biased by small sample sizes.

    PubMed

    Nazareno, Alison G; Jump, Alistair S

    2012-06-01

    Predicted parallel impacts of habitat fragmentation on genes and species lie at the core of conservation biology, yet tests of this rule are rare. In a recent article in Ecology Letters, Struebig et al. (2011) report that declining genetic diversity accompanies declining species diversity in tropical forest fragments. However, this study estimates diversity in many populations through extrapolation from very small sample sizes. Using the data of this recent work, we show that results estimated from the smallest sample sizes drive the species-genetic diversity correlation (SGDC), owing to a false-positive association between habitat fragmentation and loss of genetic diversity. Small sample sizes are a persistent problem in habitat fragmentation studies, the results of which often do not fit simple theoretical models. It is essential, therefore, that data assessing the proposed SGDC are sufficient in order that conclusions be robust.

  16. Sea level, dinosaur diversity and sampling biases: investigating the ‘common cause’ hypothesis in the terrestrial realm

    PubMed Central

    Butler, Richard J.; Benson, Roger B. J.; Carrano, Matthew T.; Mannion, Philip D.; Upchurch, Paul

    2011-01-01

    The fossil record is our primary window onto the diversification of ancient life, but there are widespread concerns that sampling biases may distort observed palaeodiversity counts. Such concerns have been reinforced by numerous studies that found correlations between measures of sampling intensity and observed diversity. However, correlation does not necessarily mean that sampling controls observed diversity: an alternative view is that both sampling and diversity may be driven by some common factor (e.g. variation in continental flooding driven by sea level). The latter is known as the ‘common cause’ hypothesis. Here, we present quantitative analyses of the relationships between dinosaur diversity, sampling of the dinosaur fossil record, and changes in continental flooding and sea level, providing new insights into terrestrial common cause. Although raw data show significant correlations between continental flooding/sea level and both observed diversity and sampling, these correlations do not survive detrending or removal of short-term autocorrelation. By contrast, the strong correlation between diversity and sampling is robust to various data transformations. Correlations between continental flooding/sea level and taxic diversity/sampling result from a shared upward trend in all data series, and short-term changes in continental flooding/sea level and diversity/sampling do not correlate. The hypothesis that global dinosaur diversity is tied to sea-level fluctuations is poorly supported, and terrestrial common cause is unsubstantiated as currently conceived. Instead, we consider variation in sampling to be the preferred null hypothesis for short-term diversity variation in the Mesozoic terrestrial realm. PMID:20880889

  17. Correction for Attenuation with Biased Reliability Estimates and Correlated Errors in Populations and Samples

    ERIC Educational Resources Information Center

    Zimmerman, Donald W.

    2007-01-01

    Properties of the Spearman correction for attenuation were investigated using Monte Carlo methods, under conditions where correlations between error scores exist as a population parameter and also where correlated errors arise by chance in random sampling. Equations allowing for all possible dependence among true and error scores on two tests at…

  18. Sample Size Effects on Bias in CE50 and CE90

    DTIC Science & Technology

    2016-09-01

    OMB No. 0704-0188 Public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for...information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing...SUPPLEMENTARY NOTES CA: Air Force Test Center Edwards AFB CA CC: 012100 14. ABSTRACT Small samples affect estimates of the ninetieth

  19. Small Sample Performance of Bias-corrected Sandwich Estimators for Cluster-Randomized Trials with Binary Outcomes

    PubMed Central

    Li, Peng; Redden, David T.

    2014-01-01

    SUMMARY The sandwich estimator in generalized estimating equations (GEE) approach underestimates the true variance in small samples and consequently results in inflated type I error rates in hypothesis testing. This fact limits the application of the GEE in cluster-randomized trials (CRTs) with few clusters. Under various CRT scenarios with correlated binary outcomes, we evaluate the small sample properties of the GEE Wald tests using bias-corrected sandwich estimators. Our results suggest that the GEE Wald z test should be avoided in the analyses of CRTs with few clusters even when bias-corrected sandwich estimators are used. With t-distribution approximation, the Kauermann and Carroll (KC)-correction can keep the test size to nominal levels even when the number of clusters is as low as 10, and is robust to the moderate variation of the cluster sizes. However, in cases with large variations in cluster sizes, the Fay and Graubard (FG)-correction should be used instead. Furthermore, we derive a formula to calculate the power and minimum total number of clusters one needs using the t test and KC-correction for the CRTs with binary outcomes. The power levels as predicted by the proposed formula agree well with the empirical powers from the simulations. The proposed methods are illustrated using real CRT data. We conclude that with appropriate control of type I error rates under small sample sizes, we recommend the use of GEE approach in CRTs with binary outcomes due to fewer assumptions and robustness to the misspecification of the covariance structure. PMID:25345738

  20. Extent of sample loss on the sampling device and the resulting experimental biases when collecting volatile fatty acids (VFAs) in air using sorbent tubes.

    PubMed

    Kim, Yong-Hyun; Kim, Ki-Hyun

    2013-08-20

    Not all volatile organic compounds (VOCs) are suitable for sampling from air onto sorbent tubes (ST) with subsequent analysis by thermal desorption (TD) with gas chromatography (GC). Some compounds (such as C2 hydrocarbons) are too volatile for quantitative retention by sorbents at ambient temperature, while others are too reactive - either for storage stability on the tubes (post-sampling) or for thermal desorption/GC analysis. Volatile fatty acids (VFAs) are one of the compound groups that present a challenge to sorbent tube sampling. In this study, we evaluated sample losses on the inner wall surface of the sorbent tube sampler. The sorptive losses of five VFA (acetic, propionic, n-butyric, i-valeric, and n-valeric acid) were tested using two types of tubes (stainless steel and quartz), each packed with three sorbent beds arranged in order of sorbent strength from the sampling end of the tube (Tenax TA, Carbopack B, and Carbopack X). It showed significantly higher losses of VFAs in both liquid phase and vapor phase when using stainless steel tube samplers. These losses were also seen if vapor-phase fatty acids were passed through empty stainless steel tubing and increased dramatically with increasing molecular weight, e.g., losses of 33.6% (acetic acid) to 97.5% (n-valeric acid). Similar losses of VFAs were also observed from headspace sampling of cheese products. Considering that stainless steel sampling tubes are still used extensively by many researchers, their replacement with quartz tubes is recommended to reduce systematic biases in collecting VFA samples or in their calibration.

  1. Reactivity-worth estimates of the OSMOSE samples in the MINERVE reactor R1-MOX, R2-UO2 and MORGANE/R configurations.

    SciTech Connect

    Zhong, Z.; Klann, R. T.; Nuclear Engineering Division

    2007-08-03

    An initial series of calculations of the reactivity-worth of the OSMOSE samples in the MINERVE reactor with the R2-UO2 and MORGANE/R core configuration were completed. The calculation model was generated using the lattice physics code DRAGON. In addition, an initial comparison of calculated values to experimental measurements was performed based on preliminary results for the R1-MOX configuration.

  2. A unified thermostat scheme for efficient configurational sampling for classical/quantum canonical ensembles via molecular dynamics

    NASA Astrophysics Data System (ADS)

    Zhang, Zhijun; Liu, Xinzijian; Chen, Zifei; Zheng, Haifeng; Yan, Kangyu; Liu, Jian

    2017-07-01

    We show a unified second-order scheme for constructing simple, robust, and accurate algorithms for typical thermostats for configurational sampling for the canonical ensemble. When Langevin dynamics is used, the scheme leads to the BAOAB algorithm that has been recently investigated. We show that the scheme is also useful for other types of thermostats, such as the Andersen thermostat and Nosé-Hoover chain, regardless of whether the thermostat is deterministic or stochastic. In addition to analytical analysis, two 1-dimensional models and three typical real molecular systems that range from the gas phase, clusters, to the condensed phase are used in numerical examples for demonstration. Accuracy may be increased by an order of magnitude for estimating coordinate-dependent properties in molecular dynamics (when the same time interval is used), irrespective of which type of thermostat is applied. The scheme is especially useful for path integral molecular dynamics because it consistently improves the efficiency for evaluating all thermodynamic properties for any type of thermostat.

  3. Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing.

    PubMed

    Vrancken, Bram; Trovão, Nídia Sequeira; Baele, Guy; van Wijngaerden, Eric; Vandamme, Anne-Mieke; van Laethem, Kristel; Lemey, Philippe

    2016-01-07

    Genetic analyses play a central role in infectious disease research. Massively parallelized "mechanical cloning" and sequencing technologies were quickly adopted by HIV researchers in order to broaden the understanding of the clinical importance of minor drug-resistant variants. These efforts have, however, remained largely limited to small genomic regions. The growing need to monitor multiple genome regions for drug resistance testing, as well as the obvious benefit for studying evolutionary and epidemic processes makes complete genome sequencing an important goal in viral research. In addition, a major drawback for NGS applications to RNA viruses is the need for large quantities of input DNA. Here, we use a generic overlapping amplicon-based near full-genome amplification protocol to compare low-input enzymatic fragmentation (Nextera™) with conventional mechanical shearing for Roche 454 sequencing. We find that the fragmentation method has only a modest impact on the characterization of the population composition and that for reliable results, the variation introduced at all steps of the procedure--from nucleic acid extraction to sequencing--should be taken into account, a finding that is also relevant for NGS technologies that are now more commonly used. Furthermore, by applying our protocol to deep sequence a number of pre-therapy plasma and PBMC samples, we illustrate the potential benefits of a near complete genome sequencing approach in routine genotyping.

  4. Linking questions to practices in the study of microbial pathogens: sampling bias and typing methods.

    PubMed

    Gómez-Díaz, Elena

    2009-12-01

    The importance of understanding the population genetics and evolution of microbial pathogens is increasing as a result of the spread and re-emergence of many infectious diseases and their impact for public health. In the last few years, the development of high throughput multi-gene sequence methodologies has opened new opportunities for studying pathogen populations, providing reliable and robust means for both epidemiological and evolutionary investigations. For instance, for many pathogens, multilocus sequence typing has become the "gold standard" in molecular epidemiology, allowing strain identification and discovery. However, there is a huge gap between typing a clinical collection of isolates and making inferences about their evolutionary history and population genetics. Critical issues for studying microbial pathogens such as an adequate sampling design and the appropriate selection of the genetic technique are also required, and will rely on the scale of study and the characteristics of the biological system (e.g., multi- vs. single-host pathogens and vector vs. food or air-borne pathogens). My aim here is to discuss some of these issues in more detail and illustrate how these aspects are often overlooked and easily neglected in the field. Finally, given the rapid accumulation of complete genome sequences and the increasing effort on microbiology research, it is clear that now more than ever integrative approaches bringing together epidemiology and evolutionary biology are needed for understanding the diversity of microbial pathogens.

  5. A study of total measurement error in tomographic gamma scanning to assay nuclear material with emphasis on a bias issue for low-activity samples

    SciTech Connect

    Burr, T.L.; Mercer, D.J.; Prettyman, T.H.

    1998-12-31

    Field experience with the tomographic gamma scanner to assay nuclear material suggests that the analysis techniques can significantly impact the assay uncertainty. For example, currently implemented image reconstruction methods exhibit a positive bias for low-activity samples. Preliminary studies indicate that bias reduction could be achieved at the expense of increased random error variance. In this paper, the authors examine three possible bias sources: (1) measurement error in the estimated transmission matrix, (2) the positivity constraint on the estimated mass of nuclear material, and (3) improper treatment of the measurement error structure. The authors present results from many small-scale simulation studies to examine this bias/variance tradeoff for a few image reconstruction methods in the presence of the three possible bias sources.

  6. Investigation of NA processes at reactive fringes: Sampling bias introduced by high resolution multi-level monitoring

    NASA Astrophysics Data System (ADS)

    Piepenbrink, M.; Ptak, T.; Grathwohl, P.

    2005-12-01

    Monitored natural attenuation is a potentially valuable risk-based remediation strategy for contaminated groundwater. The most important mass-removal process for natural attenuation is biodegradation. Certain zones or fringes of a contaminant plume offer supporting conditions for biodegradation: microbes, nutrients, contaminants and electron donors / acceptors are not only found together but also in the required reaction ratios. Due to this fact these areas show a relative rapid degradation and provide a significant contribution to the overall reduction of mass within the plume. As can be shown by high resolution numerical simulations of reactive transport in groundwater, the spatial distribution of these highly reactive zones, compared to the volume of the whole plume, is quite small and characterized by steep concentration gradients, which can not be detected using standard monitoring procedures. High resolution multi-level sampling (MLS) in the order of decimeters or less is an essential prerequisite for the investigation of NA processes at the reactive fringes at field scale. Furthermore, in contrast to technical remediation techniques which most often deal with high contaminant concentration levels close to the source zone, MNA relies heavily on the accuracy of the low concentration levels (down to the legal limits) measured in the plume. Quite often these data are strongly biased due to the monitoring equipment. This contribution presents results from ongoing controlled laboratory material tests and research on high resolution MLS at six field sites in different European countries. The focus was on a optimized site-specific hydraulic design and contaminant - MLS-material interaction. Most acceptable solutions (which means MLS resolution in the order of 0.1m) were found using sampling tubes with a small inner diameter (3-4mm). This results in a small stagnant water volume prior to sampling, but is still not problematic with respect to the flow induced

  7. Composite Partial Likelihood Estimation Under Length-Biased Sampling, With Application to a Prevalent Cohort Study of Dementia

    PubMed Central

    Huang, Chiung-Yu; Qin, Jing

    2013-01-01

    The Canadian Study of Health and Aging (CSHA) employed a prevalent cohort design to study survival after onset of dementia, where patients with dementia were sampled and the onset time of dementia was determined retrospectively. The prevalent cohort sampling scheme favors individuals who survive longer. Thus, the observed survival times are subject to length bias. In recent years, there has been a rising interest in developing estimation procedures for prevalent cohort survival data that not only account for length bias but also actually exploit the incidence distribution of the disease to improve efficiency. This article considers semiparametric estimation of the Cox model for the time from dementia onset to death under a stationarity assumption with respect to the disease incidence. Under the stationarity condition, the semiparametric maximum likelihood estimation is expected to be fully efficient yet difficult to perform for statistical practitioners, as the likelihood depends on the baseline hazard function in a complicated way. Moreover, the asymptotic properties of the semiparametric maximum likelihood estimator are not well-studied. Motivated by the composite likelihood method (Besag 1974), we develop a composite partial likelihood method that retains the simplicity of the popular partial likelihood estimator and can be easily performed using standard statistical software. When applied to the CSHA data, the proposed method estimates a significant difference in survival between the vascular dementia group and the possible Alzheimer’s disease group, while the partial likelihood method for left-truncated and right-censored data yields a greater standard error and a 95% confidence interval covering 0, thus highlighting the practical value of employing a more efficient methodology. To check the assumption of stable disease for the CSHA data, we also present new graphical and numerical tests in the article. The R code used to obtain the maximum composite partial

  8. Spatial variability of "Did You Feel It?" intensity data: insights into sampling biases in historical earthquake intensity distributions

    USGS Publications Warehouse

    Hough, Susan E.

    2013-01-01

    Recent parallel development of improved quantitative methods to analyze intensity distributions for historical earthquakes and of web‐based systems for collecting intensity data for modern earthquakes provides an opportunity to reconsider not only important individual historical earthquakes but also the overall characterization of intensity distributions for historical events. The focus of this study is a comparison between intensity distributions of historical earthquakes with those from modern earthquakes for which intensities have been determined by the U.S. Geological Survey “Did You Feel It?” (DYFI) website (see Data and Resources). As an example of a historical earthquake, I focus initially on the 1843 Marked Tree, Arkansas, event. Its magnitude has been previously estimated as 6.0–6.2. I first reevaluate the macroseismic effects of this earthquake, assigning intensities using a traditional approach, and estimate a preferred magnitude of 5.4. Modified Mercalli intensity (MMI) values for the Marked Tree earthquake are higher, on average, than those from the 2011 >Mw 5.8 Mineral, Virginia, earthquake for distances ≤500  km but comparable or lower on average at larger distances, with a smaller overall felt extent. Intensity distributions for other moderate historical earthquakes reveal similar discrepancies; the discrepancy is also even more pronounced using earlier published intensities for the 1843 earthquake. I discuss several hypotheses to explain the discrepancies, including the possibility that intensity values associated with historical earthquakes are commonly inflated due to reporting/sampling biases. A detailed consideration of the DYFI intensity distribution for the Mineral earthquake illustrates how reporting and sampling biases can account for historical earthquake intensity biases as high as two intensity units and for the qualitative difference in intensity distance decays for modern versus historical events. Thus, intensity maps for

  9. Worry or craving? A selective review of evidence for food-related attention biases in obese individuals, eating-disorder patients, restrained eaters and healthy samples.

    PubMed

    Werthmann, Jessica; Jansen, Anita; Roefs, Anne

    2015-05-01

    Living in an 'obesogenic' environment poses a serious challenge for weight maintenance. However, many people are able to maintain a healthy weight indicating that not everybody is equally susceptible to the temptations of this food environment. The way in which someone perceives and reacts to food cues, that is, cognitive processes, could underlie differences in susceptibility. An attention bias for food could be such a cognitive factor that contributes to overeating. However, an attention bias for food has also been implicated with restrained eating and eating-disorder symptomatology. The primary aim of the present review was to determine whether an attention bias for food is specifically related to obesity while also reviewing evidence for attention biases in eating-disorder patients, restrained eaters and healthy-weight individuals. Another aim was to systematically examine how selective attention for food relates (causally) to eating behaviour. Current empirical evidence on attention bias for food within obese samples, eating-disorder patients, and, even though to a lesser extent, in restrained eaters is contradictory. However, present experimental studies provide relatively consistent evidence that an attention bias for food contributes to subsequent food intake. This review highlights the need to distinguish not only between different (temporal) attention bias components, but also to take different motivations (craving v. worry) and their impact on attentional processing into account. Overall, the current state of research suggests that biased attention could be one important cognitive mechanism by which the food environment tempts us into overeating.

  10. Assessing the potential for racial bias in hair analysis for cocaine: examining the relative risk of positive outcomes when comparing urine samples to hair samples.

    PubMed

    Mieczkowski, Tom

    2011-03-20

    This article examines the conjecture that hair analysis, performed to detect cocaine use or exposure, is biased against African Americans. It does so by comparing the outcomes of 33,928 hair and 105,792 urine samples collected from both African American and white subjects. In making this comparison the analysis seeks to determine if there is a departure in rates of positive and negative outcomes when comparing the results of hair analysis for cocaine to the results from urinalysis for cocaine by racial group. It treats urine as an unbiased test. It compares both the relative ratios of positive outcomes when comparing the two groups and it calculates the relative risk of outcomes for each group for having positive or negative outcomes. The findings show that the ratios of each racial group are effectively same for hair and urine assays, and they also show that the relative risk and risk estimates for positive and negative outcomes are the same for both racial groups. Considering all samples, the cocaine positive risk estimate for the hair samples comparing the two racial groups is 3.28 and for urinalysis the risk estimate is 3.10 (Breslow-Day χ(2) .250, 1 df, p = 0.617) a non-significant difference in risk. For pre-employment samples, the cocaine positive risk estimate for the hair samples comparing the two racial groups is 3.10 and for urinalysis the risk estimate is 2.90 (Breslow-Day χ(2) .281, df = 1, p = 0.595), also a non-significant difference in risk. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  11. The proportionator: unbiased stereological estimation using biased automatic image analysis and non-uniform probability proportional to size sampling.

    PubMed

    Gardi, J E; Nyengaard, J R; Gundersen, H J G

    2008-03-01

    The proportionator is a novel and radically different approach to sampling with microscopes based on the well-known statistical theory (probability proportional to size-PPS sampling). It uses automatic image analysis, with a large range of options, to assign to every field of view in the section a weight proportional to some characteristic of the structure under study. A typical and very simple example, examined here, is the amount of color characteristic for the structure, marked with a stain with known properties. The color may be specific or not. In the recorded list of weights in all fields, the desired number of fields is sampled automatically with probability proportional to the weight and presented to the expert observer. Using any known stereological probe and estimator, the correct count in these fields leads to a simple, unbiased estimate of the total amount of structure in the sections examined, which in turn leads to any of the known stereological estimates including size distributions and spatial distributions. The unbiasedness is not a function of the assumed relation between the weight and the structure, which is in practice always a biased relation from a stereological (integral geometric) point of view. The efficiency of the proportionator depends, however, directly on this relation to be positive. The sampling and estimation procedure is simulated in sections with characteristics and various kinds of noises in possibly realistic ranges. In all cases examined, the proportionator is 2-15-fold more efficient than the common systematic, uniformly random sampling. The simulations also indicate that the lack of a simple predictor of the coefficient of error (CE) due to field-to-field variation is a more severe problem for uniform sampling strategies than anticipated. Because of its entirely different sampling strategy, based on known but non-uniform sampling probabilities, the proportionator for the first time allows the real CE at the section level to

  12. Toward Reduced Bias and Increased Utility in the Assessment of School Refusal Behavior: The Case for Diverse Samples and Evaluations of Context

    ERIC Educational Resources Information Center

    Lyon, Aaron R.; Cotler, Sheldon

    2007-01-01

    The current article reviews the literature on school refusal behavior. Definitional inconsistencies, the effects of biased assessment processes, and the consequences of the lack of ethnic, racial, and economic diversity in school refusal research samples are highlighted. An increase in the use of low-income, ethnic minority, community samples in…

  13. Using Data-Dependent Priors to Mitigate Small Sample Bias in Latent Growth Models: A Discussion and Illustration Using M"plus"

    ERIC Educational Resources Information Center

    McNeish, Daniel M.

    2016-01-01

    Mixed-effects models (MEMs) and latent growth models (LGMs) are often considered interchangeable save the discipline-specific nomenclature. Software implementations of these models, however, are not interchangeable, particularly with small sample sizes. Restricted maximum likelihood estimation that mitigates small sample bias in MEMs has not been…

  14. Using Data-Dependent Priors to Mitigate Small Sample Bias in Latent Growth Models: A Discussion and Illustration Using M"plus"

    ERIC Educational Resources Information Center

    McNeish, Daniel M.

    2016-01-01

    Mixed-effects models (MEMs) and latent growth models (LGMs) are often considered interchangeable save the discipline-specific nomenclature. Software implementations of these models, however, are not interchangeable, particularly with small sample sizes. Restricted maximum likelihood estimation that mitigates small sample bias in MEMs has not been…

  15. Toward Reduced Bias and Increased Utility in the Assessment of School Refusal Behavior: The Case for Diverse Samples and Evaluations of Context

    ERIC Educational Resources Information Center

    Lyon, Aaron R.; Cotler, Sheldon

    2007-01-01

    The current article reviews the literature on school refusal behavior. Definitional inconsistencies, the effects of biased assessment processes, and the consequences of the lack of ethnic, racial, and economic diversity in school refusal research samples are highlighted. An increase in the use of low-income, ethnic minority, community samples in…

  16. Applicability and Bias of VP/VS Estimates by P and S Differential Arrival Times of Spatially Clustered Earthquakes - why the method of Lin and Shearer (2007) will yield biased results in nearly all realistic configurations

    NASA Astrophysics Data System (ADS)

    Tilmann, F. J.; Palo, M.; Schurr, B.

    2016-12-01

    Estimating small-scale VP/VS variations at depth can be a powerful tool to infer lithology and hydration of a rock, with possible implications for frictional behavior. In principle, from the differential arrival times of P and S phases from a set of spatially clustered earthquakes, an estimate of the local VP/VS can be extracted, because the VP/VS is the scaling factor between the P and S differential times for each pair of earthquakes. We critically review the technique proposed by Lin and Shearer (2007), in which the mean value over all stations is subtracted from the differential arrival times of each pair of events in order to make the method independent of a priori information on origin times. The demeaned differential P and S arrival times are plotted on a plane, and the VP/VS ratio is estimated by fitting the points on this plane.We tested the method by both theoretical analysis and numerical simulations of P and S travel times in several velocity models. We found that the method returns exact values of VP/VS only in the case of a medium with homogeneous VP/VS , whereas, when a VP/VS gradient is present, the estimates are biased as an effect of systematic differences between P and S takeoff angles. We demonstrated that this bias arises from the demeaning of the arrival times over the stations. In layered models with VP/VS decreasing with depth, we found that VP/VS is overestimated or underestimated, respectively, for takeoff angles larger or smaller than 90°. In mosst realistic local earthquake monitoring settings, the take-off angles are not equally distributed but there will be a dominance of downward going rays, resulting in an overall bias. We calculated analytically the dependence of this bias on the takeoff angles. Additional simulations showed that the difference between the calculated and the expected VP/VS is reduced for simple horizontally layered velocity structures (<0.06), whereas it is 0.27 in a more realistic velocity model mimicking a

  17. Ethnicity and sampling bias in binge eating disorder: Black women who seek treatment have different characteristics than those who do not.

    PubMed

    Grilo, Carlos M; Lozano, Christine; Masheb, Robin M

    2005-11-01

    The current study investigated sampling bias as it affects recruited clinic samples of Black and White women with binge eating disorder (BED). Clinical characteristics of a recruited clinic sample (35 Black and 302 White consecutively evaluated women) with BED were compared with a community sample of Black and White women with BED drawn from the New England Women's Health Project. The clinic and community groups met the same definition of BED and were assessed with identical methods. Among White women, the clinic and community samples differed on some features (higher body mass index [BMI], and greater eating concerns and shape concerns in the clinic sample) but these differences reflected small to moderate effects sizes. In contrast, among Black women, the clinic sample had substantially higher levels (large effect sizes) of several features of eating disorders (eating concerns, dietary restraint, and shape concern), higher (moderate effect size) BMI, but lower frequency of binge eating (moderate effect size) than the community sample. A comparison of Black and White women within the clinic sample revealed little difference in clinical presentation, except for the significantly higher BMI among Black women. A sampling bias appears to exist between both White and Black recruited clinic samples of women with BED, although the bias appears to be substantially greater for Black women. Black women with BED who seek treatment have significantly different characteristics than those who do not.

  18. Cluster Sampling Bias in Government-Sponsored Evaluations: A Correlational Study of Employment and Welfare Pilots in England

    PubMed Central

    2016-01-01

    For pilot or experimental employment programme results to apply beyond their test bed, researchers must select ‘clusters’ (i.e. the job centres delivering the new intervention) that are reasonably representative of the whole territory. More specifically, this requirement must account for conditions that could artificially inflate the effect of a programme, such as the fluidity of the local labour market or the performance of the local job centre. Failure to achieve representativeness results in Cluster Sampling Bias (CSB). This paper makes three contributions to the literature. Theoretically, it approaches the notion of CSB as a human behaviour. It offers a comprehensive theory, whereby researchers with limited resources and conflicting priorities tend to oversample ‘effect-enhancing’ clusters when piloting a new intervention. Methodologically, it advocates for a ‘narrow and deep’ scope, as opposed to the ‘wide and shallow’ scope, which has prevailed so far. The PILOT-2 dataset was developed to test this idea. Empirically, it provides evidence on the prevalence of CSB. In conditions similar to the PILOT-2 case study, investigators (1) do not sample clusters with a view to maximise generalisability; (2) do not oversample ‘effect-enhancing’ clusters; (3) consistently oversample some clusters, including those with higher-than-average client caseloads; and (4) report their sampling decisions in an inconsistent and generally poor manner. In conclusion, although CSB is prevalent, it is still unclear whether it is intentional and meant to mislead stakeholders about the expected effect of the intervention or due to higher-level constraints or other considerations. PMID:27504823

  19. Positive bias and vacuum chamber wall effect on total electron yield measurement: A re-consideration of the sample current method

    NASA Astrophysics Data System (ADS)

    Ye, Ming; Wang, Dan; Li, Yun; He, Yong-ning; Cui, Wan-zhao; Daneshmand, Mojgan

    2017-02-01

    The measurement of the total secondary electron yield (TEY, δ) is of fundamental importance in areas such as accelerator, spacecraft, detector, and plasma system. Most of the running TEY facilities in the world are based on the kind of bias strategy. The applied bias can assist in the collection of the secondary/primary electrons. In the prevailing sample current method, the TEY is obtained by the measurement of the current from the sample to ground with a negative/positive bias applied to the sample. One of the basic assumptions in this method is that the positive bias can retain most of the electrons emitted by the sample. This assumption is generally recognized based on the seeming fact that the low energy secondary electrons dominate the emitted electrons. In this work, by considering the full electron energy spectrum including both the true secondary and backscattered electrons, we give a new insight in this TEY measurement method. Through the analytical derivation as well as the Particle-in-Cell numerical simulation, we show that it is due to the following two factors, other than the assumption mentioned above, which make the sample current method works satisfactorily: (a) the TEY relative error is related to the TEY itself in the form of | 1 - δ | / δ , which indicates a smallest error when measuring samples with TEY closest to 1; and (b) the compensation effect of the vacuum chamber wall. Analytical results agree well with numerical simulations and furthermore, we present a correction method for reducing the TEY relative error when measuring samples with TEY below 1. By sweeping the positive bias from 50 to 500 V, a flat silver sample in the as-received state with maximum TEY larger than 2 and a laser etched sample with maximum TEY close to 1 were measured for further verification. The obtained experimental results agree well with the theoretical analysis.

  20. Understanding attributional biases, emotions and self-esteem in 'poor me' paranoia: findings from an early psychosis sample.

    PubMed

    Fornells-Ambrojo, M; Garety, P A

    2009-06-01

    Trower and Chadwick's (1995) theory of two types of paranoia ('poor me' and 'bad me') provides a framework for understanding the seemingly contradictory evidence on persecutory delusions. Paranoia has been argued to defend against low self-esteem, but people with persecutory delusions report high levels of emotional distress and, in some instances, low self-worth. The current study investigates attributions and emotions in a sample of people with early psychosis who have persecutory delusions. 'Poor me' paranoia has been found to be more frequent than 'bad me' paranoia in the early stages of psychosis. Anger and a tendency to blame other people are hypothesized to characterize 'poor me' paranoia. The study had a cross-sectional design. Twenty individuals with early psychosis, 21 clinical controls with depression and 32 healthy volunteers completed a thorough assessment of emotions and attributions. The 'poor me' paranoia group showed higher levels of anger, anxiety and depression than the non-clinical control group. Self-esteem and guilt were however preserved. A tendency to blame others but not themselves was characteristic of the 'poor me' paranoia group whereas people in the clinical control group tended to self-blame for failures. Anger, but not self-esteem, was associated with an attributional bias characterized by blaming other people instead of oneself. In conclusion, anger, a previously overlooked emotion in the study of persecutory delusions, warrants further attention. The other-directed nature of this emotion highlights the potential role of interpersonal schemas in understanding paranoia.

  1. Increasingly minimal bias routing

    DOEpatents

    Bataineh, Abdulla; Court, Thomas; Roweth, Duncan

    2017-02-21

    A system and algorithm configured to generate diversity at the traffic source so that packets are uniformly distributed over all of the available paths, but to increase the likelihood of taking a minimal path with each hop the packet takes. This is achieved by configuring routing biases so as to prefer non-minimal paths at the injection point, but increasingly prefer minimal paths as the packet proceeds, referred to herein as Increasing Minimal Bias (IMB).

  2. The impact of exposure-biased sampling designs on detection of gene-environment interactions in case-control studies with potential exposure misclassification.

    PubMed

    Stenzel, Stephanie L; Ahn, Jaeil; Boonstra, Philip S; Gruber, Stephen B; Mukherjee, Bhramar

    2015-05-01

    With limited funding and biological specimen availability, choosing an optimal sampling design to maximize power for detecting gene-by-environment (G-E) interactions is critical. Exposure-enriched sampling is often used to select subjects with rare exposures for genotyping to enhance power for tests of G-E effects. However, exposure misclassification (MC) combined with biased sampling can affect characteristics of tests for G-E interaction and joint tests for marginal association and G-E interaction. Here, we characterize the impact of exposure-biased sampling under conditions of perfect exposure information and exposure MC on properties of several methods for conducting inference. We assess the Type I error, power, bias, and mean squared error properties of case-only, case-control, and empirical Bayes methods for testing/estimating G-E interaction and a joint test for marginal G (or E) effect and G-E interaction across three biased sampling schemes. Properties are evaluated via empirical simulation studies. With perfect exposure information, exposure-enriched sampling schemes enhance power as compared to random selection of subjects irrespective of exposure prevalence but yield bias in estimation of the G-E interaction and marginal E parameters. Exposure MC modifies the relative performance of sampling designs when compared to the case of perfect exposure information. Those conducting G-E interaction studies should be aware of exposure MC properties and the prevalence of exposure when choosing an ideal sampling scheme and method for characterizing G-E interactions and joint effects.

  3. Systematic bias in predictions of new drugs' budget impact: analysis of a sample of recent US drug launches.

    PubMed

    Broder, Michael S; Zambrano, Jenelle M; Lee, Jackie; Marken, Richard S

    2017-05-03

    Expectations about the budget impact of new drug launches may affect payer behavior and ultimately consumer costs. Therefore, we evaluated the accuracy of pre-launch US budget impact estimates for a sample of new drugs. We searched for publicly available budget impact estimates made pre-launch for drugs approved in the US from 1 September 2010 to 1 September 2015 and compared them to actual sales. Accuracy was calculated as the ratio of pre-launch estimate to actual sales. Quantitative analyses, including multivariate regressions, were used to identify factors associated with accuracy. We identified 25 budget impact estimates: 23 for one of 14 individual drugs and 2 for the category of PCSK9 inhibitors. The ratios of predicted to actual budget impact ranged from 0.2 (estimate was 20% of sales) for secukinumab to 37.5 (estimate was 37.5 × sales) for PCSK9 inhibitors. Mean ratio was 5.5. In multivariate analyses, larger eligible population, more recent estimate year (e.g. 2015 vs. 2012), and being first in class, were associated with statistically significant, greater overestimation of budget impact. For every $5.5 of predicted cost, there was $1 of actual cost to the healthcare system. This study, although based on a small, non-random sample, suggests possible cognitive bias on the part of the estimators. Overestimating budget impact may lead to early access restrictions, higher copays, and other changes that ultimately impact patients. Analysts and non-profits should be attuned to likely sources of error in order to improve their predictions.

  4. Towards reducing the cloud-induced sampling biases in MODIS LST data: a case study from Greenland

    NASA Astrophysics Data System (ADS)

    Karami, M.; Hansen, B. U.

    2016-12-01

    Satellite-driven Land Surface Temperature (LST) datasets are essential for characterizing climate change impacts on terrestrial ecosystems, as well as a wide range of surface-atmosphere studies. In the past one and a half decade, NASA's Moderate Resolution Imaging Spectroradiometer (MODIS) has provided the scientific community with LST estimates on a global scale with reasonable spatial resolution and revisit time. However, the use of MODIS LST for climate studies is complicated by the simple fact that the observations can only be made under clear-sky conditions. In regions with frequent overcast skies, this can result in the calculated climatic variables deviating from the actual surface conditions. In the present study, we propose and validate a framework based on model-driven downwelling radiation data from ERA-Interim and instantenous LST observations from both MODIS Terra and Aqua, in order to minimize the clear-sky sampling bias. The framework is validated on a cloud-affected MODIS scene covering parts of Greenland (h15v02), and by incorporating in-situ data from a number of monitoring stations in the area. The results indicate that the proposed method is able to increase the number of daily LST estimates by a factor of 2.07 and reduce the skewnewss of monthly distribution of the successful estimates by a factor of 0.22. Considering that these improvements are achieved mainly through introducing data from partially overcast days, the estimated climatic variables show better agreement with the ground truth. The overall accuracy of the model in estimating in-situ mean daily LST remained satisfactory even after incoprporating the daily downweling radiation from ERA-interim (RMSE=0.41 °K, R-squared=0.992). Nonetheless, since technical constraints are expected to continue limiting the use of high temporal resolution satellites in high latitudes, more research is required to quantify and deal with various types of cloud-induced biases present in the data from

  5. Sampling biases of the BG-sentinel trap with respect to physiology, age, and body size of adult Aedes aegypti (Diptera: Culicidae).

    PubMed

    Ball, Tamara S; Ritchie, Scott R

    2010-07-01

    Currently, Aedes aegypti (L.) control strategies are being developed that involve manipulation of the vector at the adult stage (e.g., the use of the bacterial endosymbiont Wolbachia to shorten the life span of the vector population). These novel strategies demand adult sampling methods to measure changes in population size, structure (age, sex ratio), and, ultimately, the success of the program. Each sampling method presents certain biases. Once these biases are defined, methods used to estimate population size and structure can be calibrated accordingly, resulting in more accurate and complex estimates of the vector population. A series of mark-release-recapture experiments with adult Ae. aegypti were conducted in a large outdoor flight cage and an indoor setting in far north Queensland, Australia. The biases of the BG-Sentinel trap (BGS) were investigated across several categories, as follows: 1) mosquito age; 2) sex; 3) physiological status; and 4) body size. Biases were not detected across age groups or body sizes. A significant bias was detected across physiological groups: nulliparous females were recaptured at a significantly lower rate than all other groups except blood-fed parous females, which were also recaptured at a low rate by the BGS. Males were recaptured at a higher rate than all groups, but only a significant difference in recapture rates was observed between males and nulliparous females. Previous studies show that the BGS is a highly effective tool for Ae. aegypti surveillance. The BGS proves to be a reliable tool in Ae. aegypti surveillance with consistent sampling outcomes. The sampling bias of the BGS is measurable and can be used to generate more accurate estimates of the adult population and its attributes.

  6. The risk of bias and sample size of trials of spinal manipulative therapy for low back and neck pain: analysis and recommendations.

    PubMed

    Rubinstein, Sidney M; van Eekelen, Rik; Oosterhuis, Teddy; de Boer, Michiel R; Ostelo, Raymond W J G; van Tulder, Maurits W

    2014-10-01

    The purpose of this study was to evaluate changes in methodological quality and sample size in randomized controlled trials (RCTs) of spinal manipulative therapy (SMT) for neck and low back pain over a specified period. A secondary purpose was to make recommendations for improvement for future SMT trials based upon our findings. Randomized controlled trials that examined the effect of SMT in adults with neck and/or low back pain and reported at least 1 patient-reported outcome measure were included. Studies were identified from recent Cochrane reviews of SMT, and an update of the literature was conducted (March 2013). Risk of bias was assessed using the 12-item criteria recommended by the Cochrane Back Review Group. In addition, sample size was examined. The relationship between the overall risk of bias and sample size over time was evaluated using regression analyses, and RCTs were grouped into periods (epochs) of approximately 5 years. In total, 105 RCTs were included, of which 41 (39%) were considered to have a low risk of bias. There is significant improvement in the mean risk of bias over time (P < .05), which is the most profound for items related to selection bias and, to a lesser extent, attrition and selective outcome reporting bias. Furthermore, although there is no significant increase in sample size over time (overall P = .8), the proportion of studies that performed an a priori sample size calculation is increasing statistically (odds ratio, 2.1; confidence interval, 1.5-3.0). Sensitivity analyses suggest no appreciable difference between studies for neck or low back pain for risk of bias or sample size. Methodological quality of RCTs of SMT for neck and low back pain is improving, whereas overall sample size has shown only small and nonsignificant increases. There is an increasing trend among studies to conduct sample size calculations, which relate to statistical power. Based upon these findings, 7 areas of improvement for future SMT trials are

  7. Effects of social organization, trap arrangement and density, sampling scale, and population density on bias in population size estimation using some common mark-recapture estimators

    PubMed Central

    Joshi, Amitabh; Vidya, T. N. C.

    2017-01-01

    Mark-recapture estimators are commonly used for population size estimation, and typically yield unbiased estimates for most solitary species with low to moderate home range sizes. However, these methods assume independence of captures among individuals, an assumption that is clearly violated in social species that show fission-fusion dynamics, such as the Asian elephant. In the specific case of Asian elephants, doubts have been raised about the accuracy of population size estimates. More importantly, the potential problem for the use of mark-recapture methods posed by social organization in general has not been systematically addressed. We developed an individual-based simulation framework to systematically examine the potential effects of type of social organization, as well as other factors such as trap density and arrangement, spatial scale of sampling, and population density, on bias in population sizes estimated by POPAN, Robust Design, and Robust Design with detection heterogeneity. In the present study, we ran simulations with biological, demographic and ecological parameters relevant to Asian elephant populations, but the simulation framework is easily extended to address questions relevant to other social species. We collected capture history data from the simulations, and used those data to test for bias in population size estimation. Social organization significantly affected bias in most analyses, but the effect sizes were variable, depending on other factors. Social organization tended to introduce large bias when trap arrangement was uniform and sampling effort was low. POPAN clearly outperformed the two Robust Design models we tested, yielding close to zero bias if traps were arranged at random in the study area, and when population density and trap density were not too low. Social organization did not have a major effect on bias for these parameter combinations at which POPAN gave more or less unbiased population size estimates. Therefore, the

  8. Effects of social organization, trap arrangement and density, sampling scale, and population density on bias in population size estimation using some common mark-recapture estimators.

    PubMed

    Gupta, Manan; Joshi, Amitabh; Vidya, T N C

    2017-01-01

    Mark-recapture estimators are commonly used for population size estimation, and typically yield unbiased estimates for most solitary species with low to moderate home range sizes. However, these methods assume independence of captures among individuals, an assumption that is clearly violated in social species that show fission-fusion dynamics, such as the Asian elephant. In the specific case of Asian elephants, doubts have been raised about the accuracy of population size estimates. More importantly, the potential problem for the use of mark-recapture methods posed by social organization in general has not been systematically addressed. We developed an individual-based simulation framework to systematically examine the potential effects of type of social organization, as well as other factors such as trap density and arrangement, spatial scale of sampling, and population density, on bias in population sizes estimated by POPAN, Robust Design, and Robust Design with detection heterogeneity. In the present study, we ran simulations with biological, demographic and ecological parameters relevant to Asian elephant populations, but the simulation framework is easily extended to address questions relevant to other social species. We collected capture history data from the simulations, and used those data to test for bias in population size estimation. Social organization significantly affected bias in most analyses, but the effect sizes were variable, depending on other factors. Social organization tended to introduce large bias when trap arrangement was uniform and sampling effort was low. POPAN clearly outperformed the two Robust Design models we tested, yielding close to zero bias if traps were arranged at random in the study area, and when population density and trap density were not too low. Social organization did not have a major effect on bias for these parameter combinations at which POPAN gave more or less unbiased population size estimates. Therefore, the

  9. The Effects of a Delayed Incentive on Response Rates, Response Mode, Data Quality, and Sample Bias in a Nationally Representative Mixed Mode Study

    ERIC Educational Resources Information Center

    McGonagle, Katherine A.; Freedman, Vicki A.

    2017-01-01

    This article describes the results of an experiment designed to examine the impact of the use and amount of delayed unconditional incentives in a mixed mode (push to web) supplement on response rates, response mode, data quality, and sample bias. The supplement was administered to individuals who participate in the U.S. Panel Study of Income…

  10. Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method.

    PubMed

    Cao, Youfang; Liang, Jie

    2013-07-14

    Critical events that occur rarely in biological processes are of great importance, but are challenging to study using Monte Carlo simulation. By introducing biases to reaction selection and reaction rates, weighted stochastic simulation algorithms based on importance sampling allow rare events to be sampled more effectively. However, existing methods do not address the important issue of barrier crossing, which often arises from multistable networks and systems with complex probability landscape. In addition, the proliferation of parameters and the associated computing cost pose significant problems. Here we introduce a general theoretical framework for obtaining optimized biases in sampling individual reactions for estimating probabilities of rare events. We further describe a practical algorithm called adaptively biased sequential importance sampling (ABSIS) method for efficient probability estimation. By adopting a look-ahead strategy and by enumerating short paths from the current state, we estimate the reaction-specific and state-specific forward and backward moving probabilities of the system, which are then used to bias reaction selections. The ABSIS algorithm can automatically detect barrier-crossing regions, and can adjust bias adaptively at different steps of the sampling process, with bias determined by the outcome of exhaustively generated short paths. In addition, there are only two bias parameters to be determined, regardless of the number of the reactions and the complexity of the network. We have applied the ABSIS method to four biochemical networks: the birth-death process, the reversible isomerization, the bistable Schlögl model, and the enzymatic futile cycle model. For comparison, we have also applied the finite buffer discrete chemical master equation (dCME) method recently developed to obtain exact numerical solutions of the underlying discrete chemical master equations of these problems. This allows us to assess sampling results objectively

  11. Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method

    PubMed Central

    Cao, Youfang; Liang, Jie

    2013-01-01

    Critical events that occur rarely in biological processes are of great importance, but are challenging to study using Monte Carlo simulation. By introducing biases to reaction selection and reaction rates, weighted stochastic simulation algorithms based on importance sampling allow rare events to be sampled more effectively. However, existing methods do not address the important issue of barrier crossing, which often arises from multistable networks and systems with complex probability landscape. In addition, the proliferation of parameters and the associated computing cost pose significant problems. Here we introduce a general theoretical framework for obtaining optimized biases in sampling individual reactions for estimating probabilities of rare events. We further describe a practical algorithm called adaptively biased sequential importance sampling (ABSIS) method for efficient probability estimation. By adopting a look-ahead strategy and by enumerating short paths from the current state, we estimate the reaction-specific and state-specific forward and backward moving probabilities of the system, which are then used to bias reaction selections. The ABSIS algorithm can automatically detect barrier-crossing regions, and can adjust bias adaptively at different steps of the sampling process, with bias determined by the outcome of exhaustively generated short paths. In addition, there are only two bias parameters to be determined, regardless of the number of the reactions and the complexity of the network. We have applied the ABSIS method to four biochemical networks: the birth-death process, the reversible isomerization, the bistable Schlögl model, and the enzymatic futile cycle model. For comparison, we have also applied the finite buffer discrete chemical master equation (dCME) method recently developed to obtain exact numerical solutions of the underlying discrete chemical master equations of these problems. This allows us to assess sampling results objectively

  12. Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method

    NASA Astrophysics Data System (ADS)

    Cao, Youfang; Liang, Jie

    2013-07-01

    Critical events that occur rarely in biological processes are of great importance, but are challenging to study using Monte Carlo simulation. By introducing biases to reaction selection and reaction rates, weighted stochastic simulation algorithms based on importance sampling allow rare events to be sampled more effectively. However, existing methods do not address the important issue of barrier crossing, which often arises from multistable networks and systems with complex probability landscape. In addition, the proliferation of parameters and the associated computing cost pose significant problems. Here we introduce a general theoretical framework for obtaining optimized biases in sampling individual reactions for estimating probabilities of rare events. We further describe a practical algorithm called adaptively biased sequential importance sampling (ABSIS) method for efficient probability estimation. By adopting a look-ahead strategy and by enumerating short paths from the current state, we estimate the reaction-specific and state-specific forward and backward moving probabilities of the system, which are then used to bias reaction selections. The ABSIS algorithm can automatically detect barrier-crossing regions, and can adjust bias adaptively at different steps of the sampling process, with bias determined by the outcome of exhaustively generated short paths. In addition, there are only two bias parameters to be determined, regardless of the number of the reactions and the complexity of the network. We have applied the ABSIS method to four biochemical networks: the birth-death process, the reversible isomerization, the bistable Schlögl model, and the enzymatic futile cycle model. For comparison, we have also applied the finite buffer discrete chemical master equation (dCME) method recently developed to obtain exact numerical solutions of the underlying discrete chemical master equations of these problems. This allows us to assess sampling results objectively

  13. Some insights into analytical bias involved in the application of grab sampling for volatile organic compounds: a case study against used Tedlar bags.

    PubMed

    Ghosh, Samik; Kim, Ki-Hyun; Sohn, Jong Ryeul

    2011-01-01

    In this study, we have examined the patterns of VOCs released from used Tedlar bags that were once used for the collection under strong source activities. In this way, we attempted to account for the possible bias associated with the repetitive use of Tedlar bags. To this end, we selected the bags that were never heated. All of these target bags were used in ambient temperature (typically at or below 30°C). These bags were also dealt carefully to avoid any mechanical abrasion. This study will provide the essential information regarding the interaction between VOCs and Tedlar bag materials as a potential source of bias in bag sampling approaches.

  14. Some Insights into Analytical Bias Involved in the Application of Grab Sampling for Volatile Organic Compounds: A Case Study against Used Tedlar Bags

    PubMed Central

    Ghosh, Samik; Kim, Ki-Hyun; Sohn, Jong Ryeul

    2011-01-01

    In this study, we have examined the patterns of VOCs released from used Tedlar bags that were once used for the collection under strong source activities. In this way, we attempted to account for the possible bias associated with the repetitive use of Tedlar bags. To this end, we selected the bags that were never heated. All of these target bags were used in ambient temperature (typically at or below 30°C). These bags were also dealt carefully to avoid any mechanical abrasion. This study will provide the essential information regarding the interaction between VOCs and Tedlar bag materials as a potential source of bias in bag sampling approaches. PMID:22235175

  15. Correcting for bias of molecular confinement parameters induced by small-time-series sample sizes in single-molecule trajectories containing measurement noise.

    PubMed

    Calderon, Christopher P

    2013-07-01

    Several single-molecule studies aim to reliably extract parameters characterizing molecular confinement or transient kinetic trapping from experimental observations. Pioneering works from single-particle tracking (SPT) in membrane diffusion studies [Kusumi et al., Biophys. J. 65, 2021 (1993)] appealed to mean square displacement (MSD) tools for extracting diffusivity and other parameters quantifying the degree of confinement. More recently, the practical utility of systematically treating multiple noise sources (including noise induced by random photon counts) through likelihood techniques has been more broadly realized in the SPT community. However, bias induced by finite-time-series sample sizes (unavoidable in practice) has not received great attention. Mitigating parameter bias induced by finite sampling is important to any scientific endeavor aiming for high accuracy, but correcting for bias is also often an important step in the construction of optimal parameter estimates. In this article, it is demonstrated how a popular model of confinement can be corrected for finite-sample bias in situations where the underlying data exhibit Brownian diffusion and observations are measured with non-negligible experimental noise (e.g., noise induced by finite photon counts). The work of Tang and Chen [J. Econometrics 149, 65 (2009)] is extended to correct for bias in the estimated "corral radius" (a parameter commonly used to quantify confinement in SPT studies) in the presence of measurement noise. It is shown that the approach presented is capable of reliably extracting the corral radius using only hundreds of discretely sampled observations in situations where other methods (including MSD and Bayesian techniques) would encounter serious difficulties. The ability to accurately statistically characterize transient confinement suggests additional techniques for quantifying confined and/or hop diffusion in complex environments.

  16. Effect of additional sample bias in Meshed Plasma Immersion Ion Deposition (MPIID) on microstructural, surface and mechanical properties of Si-DLC films

    NASA Astrophysics Data System (ADS)

    Wu, Mingzhong; Tian, Xiubo; Li, Muqin; Gong, Chunzhi; Wei, Ronghua

    2016-07-01

    Meshed Plasma Immersion Ion Deposition (MPIID) using cage-like hollow cathode discharge is a modified process of conventional PIID, but it allows the deposition of thick diamond-like carbon (DLC) films (up to 50 μm) at a high deposition rate (up to 6.5 μm/h). To further improve the DLC film properties, a new approach to the MPIID process is proposed, in which the energy of ions incident to the sample surface can be independently controlled by an additional voltage applied between the samples and the metal meshed cage. In this study, the meshed cage was biased with a pulsed DC power supply at -1350 V peak voltage for the plasma generation, while the samples inside the cage were biased with a DC voltage from 0 V to -500 V with respect to the cage to study its effect. Si-DLC films were synthesized with a mixture of Ar, C2H2 and tetramethylsilane (TMS). After the depositions, scanning electron microscopy (SEM), atomic force microscopy (AFM), X-ray photoelectrons spectroscopy (XPS), Raman spectroscopy and nanoindentation were used to study the morphology, surface roughness, chemical bonding and structure, and the surface hardness as well as the modulus of elasticity of the Si-DLC films. It was observed that the intense ion bombardment significantly densified the films, reduced the surface roughness, reduced the H and Si contents, and increased the nanohardness (H) and modulus of elasticity (E), whereas the deposition rate decreased slightly. Using the H and E data, high values of H3/E2 and H/E were obtained on the biased films, indicating the potential excellent mechanical and tribological properties of the films. In this paper, the effects of the sample bias voltage on the film properties are discussed in detail and the optimal bias voltage is presented.

  17. Correcting for bias of molecular confinement parameters induced by small-time-series sample sizes in single-molecule trajectories containing measurement noise

    NASA Astrophysics Data System (ADS)

    Calderon, Christopher P.

    2013-07-01

    Several single-molecule studies aim to reliably extract parameters characterizing molecular confinement or transient kinetic trapping from experimental observations. Pioneering works from single-particle tracking (SPT) in membrane diffusion studies [Kusumi , Biophys. J.BIOJAU0006-349510.1016/S0006-3495(93)81253-0 65, 2021 (1993)] appealed to mean square displacement (MSD) tools for extracting diffusivity and other parameters quantifying the degree of confinement. More recently, the practical utility of systematically treating multiple noise sources (including noise induced by random photon counts) through likelihood techniques has been more broadly realized in the SPT community. However, bias induced by finite-time-series sample sizes (unavoidable in practice) has not received great attention. Mitigating parameter bias induced by finite sampling is important to any scientific endeavor aiming for high accuracy, but correcting for bias is also often an important step in the construction of optimal parameter estimates. In this article, it is demonstrated how a popular model of confinement can be corrected for finite-sample bias in situations where the underlying data exhibit Brownian diffusion and observations are measured with non-negligible experimental noise (e.g., noise induced by finite photon counts). The work of Tang and Chen [J. Econometrics0304-407610.1016/j.jeconom.2008.11.001 149, 65 (2009)] is extended to correct for bias in the estimated “corral radius” (a parameter commonly used to quantify confinement in SPT studies) in the presence of measurement noise. It is shown that the approach presented is capable of reliably extracting the corral radius using only hundreds of discretely sampled observations in situations where other methods (including MSD and Bayesian techniques) would encounter serious difficulties. The ability to accurately statistically characterize transient confinement suggests additional techniques for quantifying confined and/or hop

  18. Communication: Estimating the initial biasing potential for λ-local-elevation umbrella-sampling (λ-LEUS) simulations via slow growth

    SciTech Connect

    Bieler, Noah S.; Hünenberger, Philippe H.

    2014-11-28

    In a recent article [Bieler et al., J. Chem. Theory Comput. 10, 3006–3022 (2014)], we introduced a combination of the λ-dynamics (λD) approach for calculating alchemical free-energy differences and of the local-elevation umbrella-sampling (LEUS) memory-based biasing method to enhance the sampling along the alchemical coordinate. The combined scheme, referred to as λ-LEUS, was applied to the perturbation of hydroquinone to benzene in water as a test system, and found to represent an improvement over thermodynamic integration (TI) in terms of sampling efficiency at equivalent accuracy. However, the preoptimization of the biasing potential required in the λ-LEUS method requires “filling up” all the basins in the potential of mean force. This introduces a non-productive pre-sampling time that is system-dependent, and generally exceeds the corresponding equilibration time in a TI calculation. In this letter, a remedy is proposed to this problem, termed the slow growth memory guessing (SGMG) approach. Instead of initializing the biasing potential to zero at the start of the preoptimization, an approximate potential of mean force is estimated from a short slow growth calculation, and its negative used to construct the initial memory. Considering the same test system as in the preceding article, it is shown that of the application of SGMG in λ-LEUS permits to reduce the preoptimization time by about a factor of four.

  19. Communication: Estimating the initial biasing potential for λ-local-elevation umbrella-sampling (λ-LEUS) simulations via slow growth

    NASA Astrophysics Data System (ADS)

    Bieler, Noah S.; Hünenberger, Philippe H.

    2014-11-01

    In a recent article [Bieler et al., J. Chem. Theory Comput. 10, 3006-3022 (2014)], we introduced a combination of the λ-dynamics (λD) approach for calculating alchemical free-energy differences and of the local-elevation umbrella-sampling (LEUS) memory-based biasing method to enhance the sampling along the alchemical coordinate. The combined scheme, referred to as λ-LEUS, was applied to the perturbation of hydroquinone to benzene in water as a test system, and found to represent an improvement over thermodynamic integration (TI) in terms of sampling efficiency at equivalent accuracy. However, the preoptimization of the biasing potential required in the λ-LEUS method requires "filling up" all the basins in the potential of mean force. This introduces a non-productive pre-sampling time that is system-dependent, and generally exceeds the corresponding equilibration time in a TI calculation. In this letter, a remedy is proposed to this problem, termed the slow growth memory guessing (SGMG) approach. Instead of initializing the biasing potential to zero at the start of the preoptimization, an approximate potential of mean force is estimated from a short slow growth calculation, and its negative used to construct the initial memory. Considering the same test system as in the preceding article, it is shown that of the application of SGMG in λ-LEUS permits to reduce the preoptimization time by about a factor of four.

  20. The gas chromatographic determination of volatile fatty acids in wastewater samples: evaluation of experimental biases in direct injection method against thermal desorption method.

    PubMed

    Ullah, Md Ahsan; Kim, Ki-Hyun; Szulejko, Jan E; Cho, Jinwoo

    2014-04-11

    The production of short-chained volatile fatty acids (VFAs) by the anaerobic bacterial digestion of sewage (wastewater) affords an excellent opportunity to alternative greener viable bio-energy fuels (i.e., microbial fuel cell). VFAs in wastewater (sewage) samples are commonly quantified through direct injection (DI) into a gas chromatograph with a flame ionization detector (GC-FID). In this study, the reliability of VFA analysis by the DI-GC method has been examined against a thermal desorption (TD-GC) method. The results indicate that the VFA concentrations determined from an aliquot from each wastewater sample by the DI-GC method were generally underestimated, e.g., reductions of 7% (acetic acid) to 93.4% (hexanoic acid) relative to the TD-GC method. The observed differences between the two methods suggest the possibly important role of the matrix effect to give rise to the negative biases in DI-GC analysis. To further explore this possibility, an ancillary experiment was performed to examine bias patterns of three DI-GC approaches. For instance, the results of the standard addition (SA) method confirm the definite role of matrix effect when analyzing wastewater samples by DI-GC. More importantly, their biases tend to increase systematically with increasing molecular weight and decreasing VFA concentrations. As such, the use of DI-GC method, if applied for the analysis of samples with a complicated matrix, needs a thorough validation to improve the reliability in data acquisition.

  1. Hidden in plain sight: bias towards sick patients when sampling patients with sufficient electronic health record data for research.

    PubMed

    Rusanov, Alexander; Weiskopf, Nicole G; Wang, Shuang; Weng, Chunhua

    2014-06-11

    To demonstrate that subject selection based on sufficient laboratory results and medication orders in electronic health records can be biased towards sick patients. Using electronic health record data from 10,000 patients who received anesthetic services at a major metropolitan tertiary care academic medical center, an affiliated hospital for women and children, and an affiliated urban primary care hospital, the correlation between patient health status and counts of days with laboratory results or medication orders, as indicated by the American Society of Anesthesiologists Physical Status Classification (ASA Class), was assessed with a Negative Binomial Regression model. Higher ASA Class was associated with more points of data: compared to ASA Class 1 patients, ASA Class 4 patients had 5.05 times the number of days with laboratory results and 6.85 times the number of days with medication orders, controlling for age, sex, emergency status, admission type, primary diagnosis, and procedure. Imposing data sufficiency requirements for subject selection allows researchers to minimize missing data when reusing electronic health records for research, but introduces a bias towards the selection of sicker patients. We demonstrated the relationship between patient health and quantity of data, which may result in a systematic bias towards the selection of sicker patients for research studies and limit the external validity of research conducted using electronic health record data. Additionally, we discovered other variables (i.e., admission status, age, emergency classification, procedure, and diagnosis) that independently affect data sufficiency.

  2. Comparison of non-landslide sampling strategies to counteract inventory-based biases within national-scale statistical landslide susceptibility models

    NASA Astrophysics Data System (ADS)

    Lima, Pedro; Steger, Stefan; Glade, Thomas

    2017-04-01

    Landslides can represent a significant threat for people and infrastructure in hilly and mountainous landscapes worldwide. The understanding and prediction of those geomorphic processes is crucial to avoid economic loses or even casualties to people and their properties. Statistical based landslide susceptibility models are well known for being highly reliant on the quality, representativeness and availability of input data. In this context, several studies indicate that the landslide inventory represents the most important input data. However each landslide mapping technique or data collection has its drawbacks. Consequently, biased landslide inventories may be commonly introduced into statistical models, especially at regional or even national scale. It remains to the researcher to be aware of potential limitations and design strategies to avoid or reduce the potential propagation of input data errors and biases influences on the modelling outcomes. Previous studies have proven that such erroneous landslide inventories may lead to unrealistic landslide susceptibility maps. We assume that one possibility to tackle systematic landslide inventory-based biases might be a concentration on sampling strategies that focus on the distribution of non-landslide locations. For this purpose, we test an approach for the Austrian territory that concentrates on a modified non-landslide sampling strategy, instead the traditional applied random sampling. It is expected that the way non-landslide locations are represented (e.g. equally over the area or within those areas where mapping campaigns have been conducted) is important to reduce a potential over- or underestimation of landslide susceptibility within specific areas caused by bias. As presumably each landslide inventory is known to be systematically incomplete, especially in those areas where no mapping campaign was previously conducted. This is also applicable to the one currently available for the Austrian territory

  3. Accuracy Sampling Design Bias on Coarse Spatial Resolution Land Cover Data in the Great Lakes Region (United States and Canada)

    EPA Science Inventory

    A number of articles have investigated the impact of sampling design on remotely sensed landcover accuracy estimates. Gong and Howarth (1990) found significant differences for Kappa accuracy values when comparing purepixel sampling, stratified random sampling, and stratified sys...

  4. Accuracy Sampling Design Bias on Coarse Spatial Resolution Land Cover Data in the Great Lakes Region (United States and Canada)

    EPA Science Inventory

    A number of articles have investigated the impact of sampling design on remotely sensed landcover accuracy estimates. Gong and Howarth (1990) found significant differences for Kappa accuracy values when comparing purepixel sampling, stratified random sampling, and stratified sys...

  5. Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells.

    PubMed

    Glatter, Timo; Ahrné, Erik; Schmidt, Alexander

    2015-11-06

    We evaluated different in-solution and FASP-based sample preparation strategies for absolute protein quantification. Label-free quantification (LFQ) was employed to compare different sample preparation strategies in the bacterium Pseudomonas aeruginosa and human embryonic kidney cells (HEK), and organismal-specific differences in general performance and enrichment of specific protein classes were noted. The original FASP protocol globally enriched for most proteins in the bacterial sample, whereas the sodium deoxycholate in-solution strategy was more efficient with HEK cells. Although detergents were found to be highly suited for global proteome analysis, higher intensities were obtained for high-abundant nucleic acid-associated protein complexes, like the ribosome and histone proteins, using guanidine hydrochloride. Importantly, we show for the first time that the observable total proteome mass of a sample strongly depends on the sample preparation protocol, with some protocols resulting in a significant underestimation of protein mass due to incomplete protein extraction of biased protein groups. Furthermore, we demonstrate that some of the observed abundance biases can be overcome by incorporating a nuclease treatment step or, alternatively, a correction factor for complementary sample preparation approaches.

  6. Influences of diurnal sampling bias on fixed-point monitoring of plankton biodiversity determined using a massively parallel sequencing-based technique.

    PubMed

    Nagai, Satoshi; Hida, Kohsuke; Urushizaki, Shingo; Onitsuka, Goh; Yasuike, Motoshige; Nakamura, Yoji; Fujiwara, Atushi; Tajimi, Seisuke; Kimoto, Katsunori; Kobayashi, Takanori; Gojobori, Takashi; Ototake, Mitsuru

    2016-02-01

    In this study, we investigated the influence of diurnal sampling bias on the community structure of plankton by comparing the biodiversity among seawater samples (n=9) obtained every 3h for 24h by using massively parallel sequencing (MPS)-based plankton monitoring at a fixed point conducted at Himedo seaport in Yatsushiro Sea, Japan. The number of raw operational taxonomy units (OTUs) and OTUs after re-sampling was 507-658 (558 ± 104, mean ± standard deviation) and 448-544 (467 ± 81), respectively, indicating high plankton biodiversity at the sampling location. The relative abundance of the top 20 OTUs in the samples from Himedo seaport was 48.8-67.7% (58.0 ± 5.8%), and the highest-ranked OTU was Pseudo-nitzschia species (Bacillariophyta) with a relative abundance of 17.3-39.2%, followed by Oithona sp. 1 and Oithona sp. 2 (Arthropoda). During seawater sampling, the semidiurnal tidal current having an amplitude of 0.3ms(-1) was dominant, and the westward residual current driven by the northeasterly wind was continuously observed during the 24-h monitoring. Therefore, the relative abundance of plankton species apparently fluctuated among the samples, but no significant difference was noted according to G-test (p>0.05). Significant differences were observed between the samples obtained from a different locality (Kusuura in Yatsushiro Sea) and at different dates, suggesting that the influence of diurnal sampling bias on plankton diversity, determined using the MPS-based survey, was not significant and acceptable.

  7. Uncertainty in biological monitoring: a framework for data collection and analysis to account for multiple sources of sampling bias

    USGS Publications Warehouse

    Ruiz-Gutierrez, Viviana; Hooten, Melvin B.; Campbell Grant, Evan H.

    2016-01-01

    Biological monitoring programmes are increasingly relying upon large volumes of citizen-science data to improve the scope and spatial coverage of information, challenging the scientific community to develop design and model-based approaches to improve inference.Recent statistical models in ecology have been developed to accommodate false-negative errors, although current work points to false-positive errors as equally important sources of bias. This is of particular concern for the success of any monitoring programme given that rates as small as 3% could lead to the overestimation of the occurrence of rare events by as much as 50%, and even small false-positive rates can severely bias estimates of occurrence dynamics.We present an integrated, computationally efficient Bayesian hierarchical model to correct for false-positive and false-negative errors in detection/non-detection data. Our model combines independent, auxiliary data sources with field observations to improve the estimation of false-positive rates, when a subset of field observations cannot be validated a posteriori or assumed as perfect. We evaluated the performance of the model across a range of occurrence rates, false-positive and false-negative errors, and quantity of auxiliary data.The model performed well under all simulated scenarios, and we were able to identify critical auxiliary data characteristics which resulted in improved inference. We applied our false-positive model to a large-scale, citizen-science monitoring programme for anurans in the north-eastern United States, using auxiliary data from an experiment designed to estimate false-positive error rates. Not correcting for false-positive rates resulted in biased estimates of occupancy in 4 of the 10 anuran species we analysed, leading to an overestimation of the average number of occupied survey routes by as much as 70%.The framework we present for data collection and analysis is able to efficiently provide reliable inference for

  8. Internal correction of hafnium oxide spectral interferences and mass bias in the determination of platinum in environmental samples using isotope dilution analysis.

    PubMed

    Rodríguez-Castrillón, José Angel; Moldovan, Mariella; García Alonso, J Ignacio

    2009-05-01

    A method has been developed for the accurate determination of platinum by isotope dilution analysis, using enriched (194)Pt, in environmental samples containing comparatively high levels of hafnium without any chemical separation. The method is based on the computation of the contribution of hafnium oxide as an independent factor in the observed isotope pattern of platinum in the spiked sample. Under these conditions, the ratio of molar fractions between natural abundance and isotopically enriched platinum was independent of the amount of hafnium present in the sample. Additionally, mass bias was corrected by an internal procedure in which the regression variance was minimised. This was possible as the mass bias factor for hafnium oxide was very close to that of platinum. The final procedure required the measurement of three platinum isotope ratios (192/194, 195/194 and 196/194) to calculate the concentration of platinum in the sample. The methodology has been validated using the reference material "BCR-723 road dust" and has been applied to different environmental matrices (road dust, air particles, bulk wet deposition and epiphytic lichens) collected in the Aspe Valley (Pyrenees Mountains). A full uncertainty budget, using Kragten's spreadsheet method, showed that the total uncertainty was limited only by the uncertainty in the measured isotope ratios and not by the uncertainties of the isotopic composition of platinum and hafnium.

  9. Aβ Monomers Transiently Sample Oligomer and Fibril-like Configurations: Ensemble Characterization Using a Combined MD/NMR Approach

    PubMed Central

    Rosenman, David J.; Connors, Christopher; Chen, Wen; Wang, Chunyu; García, Angel E.

    2013-01-01

    Amyloid β (Aβ) peptides are a primary component of fibrils and oligomers implicated in the etiology of Alzheimer’s disease (AD). However, the intrinsic flexibility of these peptides has frustrated efforts to investigate the secondary and tertiary structure of Aβ monomers, whose conformational landscapes directly contribute to the kinetics and thermodynamics of Aβ aggregation. In this work, de novo replica exchange molecular dynamics (REMD) simulations on the μs/replica timescale are used to characterize the structural ensembles of Aβ42, Aβ40, and M35-oxidized Aβ42, three physiologically relevant isoforms with substantially different aggregation properties. J-coupling data calculated from the REMD trajectories were compared to corresponding NMR-derived values acquired through two different pulse sequences, revealing that all simulations converge on the order of hundreds of ns/replica toward ensembles that yield good agreement with experiment. Though all three Aβ species adopt highly heterogeneous ensembles, these are considerably more structured compared to simulations on shorter timescales. Prominent in the C-terminus are antiparallel β-hairpins between L17-A21, A30-L36, and V39-I41, similar to oligomer and fibril intrapeptide models, that expose these hydrophobic side chains to solvent and may serve as hotspots for self-association. Compared to reduced Aβ42, the absence of a second β-hairpin in Aβ40 and the sampling of alternate β topologies by M35-oxidized Aβ42 may explain the reduced aggregation rates of these forms. A persistent V24-K28 bend motif, observed in all three species, is stabilized by buried backbone to side chain hydrogen bonds with D23 and a cross-region salt bridge between E22 and K28, highlighting the role of the familial AD-linked E22 and D23 residues in Aβ monomer folding. These characterizations help illustrate the conformational landscapes of Aβ monomers at atomic resolution and provide insight into the early stages of A

  10. Aβ monomers transiently sample oligomer and fibril-like configurations: ensemble characterization using a combined MD/NMR approach.

    PubMed

    Rosenman, David J; Connors, Christopher R; Chen, Wen; Wang, Chunyu; García, Angel E

    2013-09-23

    Amyloid β (Aβ) peptides are a primary component of fibrils and oligomers implicated in the etiology of Alzheimer's disease (AD). However, the intrinsic flexibility of these peptides has frustrated efforts to investigate the secondary and tertiary structure of Aβ monomers, whose conformational landscapes directly contribute to the kinetics and thermodynamics of Aβ aggregation. In this work, de novo replica exchange molecular dynamics (REMD) simulations on the microseconds-per-replica timescale are used to characterize the structural ensembles of Aβ42, Aβ40, and M35-oxidized Aβ42, three physiologically relevant isoforms with substantially different aggregation properties. J-coupling data calculated from the REMD trajectories were compared to corresponding NMR-derived values acquired through two different pulse sequences, revealing that all simulations converge on the order of hundreds of nanoseconds-per-replica toward ensembles that yield good agreement with experiment. Though all three Aβ species adopt highly heterogeneous ensembles, these are considerably more structured compared to simulations on shorter timescales. Prominent in the C-terminus are antiparallel β-hairpins between L17-A21, A30-L36, and V39-I41, similar to oligomer and fibril intrapeptide models that expose these hydrophobic side chains to solvent and may serve as hotspots for self-association. Compared to reduced Aβ42, the absence of a second β-hairpin in Aβ40 and the sampling of alternate β topologies by M35-oxidized Aβ42 may explain the reduced aggregation rates of these forms. A persistent V24-K28 bend motif, observed in all three species, is stabilized by buried backbone to side-chain hydrogen bonds with D23 and a cross-region salt bridge between E22 and K28, highlighting the role of the familial AD-linked E22 and D23 residues in Aβ monomer folding. These characterizations help illustrate the conformational landscapes of Aβ monomers at atomic resolution and provide insight into

  11. Correcting for Systematic Bias in Sample Estimates of Population Variances: Why Do We Divide by n-1?

    ERIC Educational Resources Information Center

    Mittag, Kathleen Cage

    An important topic presented in introductory statistics courses is the estimation of population parameters using samples. Students learn that when estimating population variances using sample data, we always get an underestimate of the population variance if we divide by n rather than n-1. One implication of this correction is that the degree of…

  12. Selection bias in dynamically-measured super-massive black hole samples: its consequences and the quest for the most fundamental relation

    NASA Astrophysics Data System (ADS)

    Shankar, Francesco; Bernardi, M.; Sheth, R. K.; Weinberg, D. H.; Miralda-Escudé, J.; Ferrarese, L.; Graham, A.; Sesana, A.; Lapi, A.; Marconi, A.; Allevato, V.; Savorgnan, G.; Laesker, R.

    2016-08-01

    We compare the set of local galaxies having dynamically measured black holes with a large, unbiased sample of galaxies extracted from the Sloan Digital Sky Survey. We confirm earlier work showing that the majority of black hole hosts have significantly higher velocity dispersions sigma than local galaxies of similar stellar mass. We use Monte-Carlo simulations to illustrate the effect on black hole scaling relations if this bias arises from the requirement that the black hole sphere of influence must be resolved to measure black hole masses with spatially resolved kinematics. We find that this selection effect artificially increases the normalization of the Mbh-sigma relation by a factor of at least ~3; the bias for the Mbh-Mstar relation is even larger. Our Monte Carlo simulations and analysis of the residuals from scaling relations both indicate that sigma is more fundamental than Mstar or effective radius. In particular, the Mbh-Mstar relation is mostly a consequence of the Mbh-sigma and sigma-Mstar relations, and is heavily biased by up to a factor of 50 at small masses. This helps resolve the discrepancy between dynamically-based black hole-galaxy scaling relations versus those of active galaxies. Our simulations also disfavour broad distributions of black hole masses at fixed sigma. Correcting for this bias suggests that the calibration factor used to estimate black hole masses in active galaxies should be reduced to values of fvir~1. Black hole mass densities should also be proportionally smaller, perhaps implying significantly higher radiative efficiencies/black hole spins. Reducing black hole masses also reduces the gravitational wave signal expected from black hole mergers.

  13. Sample selection may bias the outcome of an adolescent mental health survey: results from a five-year follow-up of 4171 adolescents.

    PubMed

    Kekkonen, V; Kivimäki, P; Valtonen, H; Hintikka, J; Tolmunen, T; Lehto, S M; Laukkanen, E

    2015-02-01

    The representativeness of the data is one of the main issues in evaluating the significance of research findings. Dropping out is common in adolescent mental health research, and may distort the results. Nevertheless, very little is known about the types of systematic bias that may affect studies in a) the informed consent phase and b) later in follow-up phases. The authors addressed this gap in knowledge in a five-year follow-up study on a sample of adolescents aged 13-18 years. The data were collected using self-report questionnaires. The baseline sample consisted of 4171 adolescents, 1827 (43.8%) of whom gave consent to be contacted for a follow-up survey, but only 797 (19.1%) participated in the follow-up. Binary logistic regression models were used to explain the participation. Young age, female gender, a high number of hobbies, good performance at school in the native language and general subjects, family disintegration such as divorce, high parental employment, and symptoms of depression and anxiety were associated with both consent and participation. However, the effect of mental health aspects was smaller than the effect of age and gender. This study confirmed the possibility of systematic selection bias by adolescents' sociodemographic characteristics. The representativeness of the study sample might have been improved by more intense recruitment strategies. Copyright © 2014 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

  14. Universal electromagnetic suspension balance with nanogramme mass resolution for measurement of sorption on small samples in top and bottom loading configurations

    NASA Astrophysics Data System (ADS)

    Norton, C. G.; Petermann, M.; Fieback, T. M.

    2017-04-01

    Determination of mass increase or decrease of very small amplitude is a task which goes hand in hand with gravimetric adsorption and absorption measurement and thermogravimetry. Samples are subjected to various process conditions and as such can experience a change in mass, i.e. when adsorbing gas from the process atmosphere, or can decrease in mass, such as when being dried or when thermal decomposition takes place. Current instruments used for such analysis, especially at high pressures, are often based on magnetic suspension balances, and have a maximum mass resolution of a few 10-6 g. This necessitates more often than not quite significant sample quantities, which can sometimes not easily be manufactured, e.g. in the case of metal organic framework adsorbents, or which in other cases do not have a sufficient specific surface area resulting in low measuring effect. A new apparatus based on a high resolution thermogravimetric analyser has been developed. This new apparatus combines very high resolution of up to a few 10-8 g with a relatively high sample mass of up to 1.5 g, whilst eliminating many of the disadvantages of the microbalances previously used in magnetic suspension balances. An interface was developed which permits free configuration of the new balance as top or bottom loading. Validation measurements of known adsorbents were subsequently performed, with sample quantities up to a factor of 174 smaller than in literature.

  15. Reducing bias in population and landscape genetic inferences: the effects of sampling related individuals and multiple life stages.

    PubMed

    Peterman, William; Brocato, Emily R; Semlitsch, Raymond D; Eggert, Lori S

    2016-01-01

    In population or landscape genetics studies, an unbiased sampling scheme is essential for generating accurate results, but logistics may lead to deviations from the sample design. Such deviations may come in the form of sampling multiple life stages. Presently, it is largely unknown what effect sampling different life stages can have on population or landscape genetic inference, or how mixing life stages can affect the parameters being measured. Additionally, the removal of siblings from a data set is considered best-practice, but direct comparisons of inferences made with and without siblings are limited. In this study, we sampled embryos, larvae, and adult Ambystoma maculatum from five ponds in Missouri, and analyzed them at 15 microsatellite loci. We calculated allelic richness, heterozygosity and effective population sizes for each life stage at each pond and tested for genetic differentiation (F ST and D C ) and isolation-by-distance (IBD) among ponds. We tested for differences in each of these measures between life stages, and in a pooled population of all life stages. All calculations were done with and without sibling pairs to assess the effect of sibling removal. We also assessed the effect of reducing the number of microsatellites used to make inference. No statistically significant differences were found among ponds or life stages for any of the population genetic measures, but patterns of IBD differed among life stages. There was significant IBD when using adult samples, but tests using embryos, larvae, or a combination of the three life stages were not significant. We found that increasing the ratio of larval or embryo samples in the analysis of genetic distance weakened the IBD relationship, and when using D C , the IBD was no longer significant when larvae and embryos exceeded 60% of the population sample. Further, power to detect an IBD relationship was reduced when fewer microsatellites were used in the analysis.

  16. How do geological sampling biases affect studies of morphological evolution in deep time? A case study of pterosaur (Reptilia: Archosauria) disparity.

    PubMed

    Butler, Richard J; Brusatte, Stephen L; Andres, Brian; Benson, Roger B J

    2012-01-01

    A fundamental contribution of paleobiology to macroevolutionary theory has been the illumination of deep time patterns of diversification. However, recent work has suggested that taxonomic diversity counts taken from the fossil record may be strongly biased by uneven spatiotemporal sampling. Although morphological diversity (disparity) is also frequently used to examine evolutionary radiations, no empirical work has yet addressed how disparity might be affected by uneven fossil record sampling. Here, we use pterosaurs (Mesozoic flying reptiles) as an exemplar group to address this problem. We calculate multiple disparity metrics based upon a comprehensive anatomical dataset including a novel phylogenetic correction for missing data, statistically compare these metrics to four geological sampling proxies, and use multiple regression modeling to assess the importance of uneven sampling and exceptional fossil deposits (Lagerstätten). We find that range-based disparity metrics are strongly affected by uneven fossil record sampling, and should therefore be interpreted cautiously. The robustness of variance-based metrics to sample size and geological sampling suggests that they can be more confidently interpreted as reflecting true biological signals. In addition, our results highlight the problem of high levels of missing data for disparity analyses, indicating a pressing need for more theoretical and empirical work.

  17. Bias properties of extragalactic distance indicators. 3: Analysis of Tully-Fisher distances for the Mathewson-Ford-Buchhorn sample of 1355 galaxies

    NASA Astrophysics Data System (ADS)

    Federspiel, Martin; Sandage, Allan; Tammann, G. A.

    1994-07-01

    The observational selection bias properties of the large Mathewson-Ford-Buchhorn (MFB) sample of axies are demonstrated by showing that the apparent Hubble constant incorrectly increases outward when determined using Tully-Fisher (TF) photometric distances that are uncorrected for bias. It is further shown that the value of H0 so determined is also multi-valued at a given redshift when it is calculated by the TF method using galaxies with differenct line widths. The method of removing this unphysical contradiction is developed following the model of the bias set out in Paper II. The model developed further here shows that the appropriate TF magnitude of a galaxy that is drawn from a flux-limited catalog not only is a function of line width but, even in the most idealistic cases, requires a triple-entry correction depending on line width, apparent magnitude, and catalog limit. Using the distance-limited subset of the data, it is shown that the mean intrinsic dispersion of a bias-free TF relation is high. The dispersion depends on line width, decreasing from sigma(M) = 0.7 mag for galaxies with rotational velocities less than 100 km s(exp-1) to sigma(M) = 0.4 mag for galaxies with rotational velocities greater than 250 km s(exp-1). These dispersions are so large that the random errors of the bias-free TF distances are too gross to detect any peculiar motions of individual galaxies, but taken together the data show again the offset of 500 km s(exp-1) fond both by Dressler & Faber and by MFB for galaxies in the direction of the putative Great Attractor but described now in a different way. The maximum amplitude of the bulk streaming motion at the Local Group is approximately 500 km s(exp-1) but the perturbation dies out, approaching the Machian frame defined by the CMB at a distance of approximately 80 Mpc (v is approximately 4000 km s-1). This decay to zero perturbation at v is approximately 4000 km s-1 argues against existing models with a single attraction at

  18. Bias properties of extragalactic distance indicators. 3: Analysis of Tully-Fisher distances for the Mathewson-Ford-Buchhorn sample of 1355 galaxies

    NASA Technical Reports Server (NTRS)

    Federspiel, Martin; Sandage, Allan; Tammann, G. A.

    1994-01-01

    The observational selection bias properties of the large Mathewson-Ford-Buchhorn (MFB) sample of axies are demonstrated by showing that the apparent Hubble constant incorrectly increases outward when determined using Tully-Fisher (TF) photometric distances that are uncorreted for bias. It is further shown that the value of H(sub 0) so determined is also multivlaued at a given redshift when it is calculated by the TF method using galaxies with differenct line widths. The method of removing this unphysical contradiction is developed following the model of the bias set out in Paper II. The model developed further here shows that the appropriate TF magnitude of a galaxy that is drawn from a flux-limited catalog not only is a function of line width but, even in the most idealistic cases, requires a triple-entry correction depending on line width, apparent magnitude, and catalog limit. Using the distance-limited subset of the data, it is shown that the mean intrinsic dispersion of a bias-free TF relation is high. The dispersion depends on line width, decreasing from sigma(M) = 0.7 mag for galaxies with rotational velocities less than 100 km s(exp-1) to sigma(M) = 0.4 mag for galaxies with rotational velocities greater than 250 km s(exp-1). These dispersions are so large that the random errors of the bias-free TF distances are too gross to detect any peculiar motions of individual galaxies, but taken together the data show again the offset of 500 km s(exp-1) fond both by Dressler & Faber and by MFB for galaxies in the direction of the putative Great Attractor but described now in a different way. The maximum amplitude of the bulk streaming motion at the Local Group is approximately 500 km s(exp-1) but the perturbation dies out, approaching the Machian frame defined by the CMB at a distance of approximately 80 Mpc (v is approximately 4000 km s(exp -1)). This decay to zero perturbation at v is approximately 4000 km s(exp -1) argues against existing models with a single

  19. Bias properties of extragalactic distance indicators. 3: Analysis of Tully-Fisher distances for the Mathewson-Ford-Buchhorn sample of 1355 galaxies

    NASA Technical Reports Server (NTRS)

    Federspiel, Martin; Sandage, Allan; Tammann, G. A.

    1994-01-01

    The observational selection bias properties of the large Mathewson-Ford-Buchhorn (MFB) sample of axies are demonstrated by showing that the apparent Hubble constant incorrectly increases outward when determined using Tully-Fisher (TF) photometric distances that are uncorreted for bias. It is further shown that the value of H(sub 0) so determined is also multivlaued at a given redshift when it is calculated by the TF method using galaxies with differenct line widths. The method of removing this unphysical contradiction is developed following the model of the bias set out in Paper II. The model developed further here shows that the appropriate TF magnitude of a galaxy that is drawn from a flux-limited catalog not only is a function of line width but, even in the most idealistic cases, requires a triple-entry correction depending on line width, apparent magnitude, and catalog limit. Using the distance-limited subset of the data, it is shown that the mean intrinsic dispersion of a bias-free TF relation is high. The dispersion depends on line width, decreasing from sigma(M) = 0.7 mag for galaxies with rotational velocities less than 100 km s(exp-1) to sigma(M) = 0.4 mag for galaxies with rotational velocities greater than 250 km s(exp-1). These dispersions are so large that the random errors of the bias-free TF distances are too gross to detect any peculiar motions of individual galaxies, but taken together the data show again the offset of 500 km s(exp-1) fond both by Dressler & Faber and by MFB for galaxies in the direction of the putative Great Attractor but described now in a different way. The maximum amplitude of the bulk streaming motion at the Local Group is approximately 500 km s(exp-1) but the perturbation dies out, approaching the Machian frame defined by the CMB at a distance of approximately 80 Mpc (v is approximately 4000 km s(exp -1)). This decay to zero perturbation at v is approximately 4000 km s(exp -1) argues against existing models with a single

  20. Statistical Effects of Doppler Beaming and Malmquist Bias on Flux-limited Samples of Compact Radio Sources

    NASA Astrophysics Data System (ADS)

    Lister, Matthew L.; Marscher, Alan P.

    1997-02-01

    We examine the effects of Doppler beaming on flux-limited samples of compact radio sources representative of relativistic jets found in active galactic nuclei (AGNs). We expand upon past studies by incorporating a luminosity function and redshift distribution for the parent population and by allowing the unbeamed synchrotron luminosity L of a relativistic jet to be related to its bulk Lorentz factor (Γ). These enhancements allow us to compare observable parameters other than simply apparent velocity with the data. The predictions of L-Γ-independent (LGI) models are compared to those of a L-Γ-dependent (LGD) scenario in which the Lorentz factor and luminosity are related by the form L ~ Γξ. This is accomplished using Monte Carlo simulations, where we compare the predicted flux density, redshift, monochromatic emitted luminosity, and apparent velocity distributions of flux-limited samples to the Caltech-Jodrell Bank sample of bright, flat-spectrum, radio core-dominated AGNs (CJ-F). The LGI model predictions are consistent with the CJ-F data if we adopt parent Lorentz factor distributions of the form N(Γ) ~ Γa, where -1.5 <~ a <~ -1.75, or, alternatively N(Γ) ~ (Γ - 1)a, where -0.5 <~ a <~ -1. These models reproduce, via selection effects, a deficit of sources having both low apparent velocity (βapp) and high monochromatic emitted luminosity (P) seen in the CJ-F sample, as reported by Vermeulen in 1995. We examine two possible cases for the LGD scenario, the first of which employs a positive correlation between unbeamed synchrotron luminosity and Lorentz factor (the LGC model), and the second of which employs an anticorrelation (the LGA model). The LGA models do not predict enough low-P sources to be consistent with the CJ-F data and do not reproduce the P versus βapp envelope. The predictions of the best-fit LGC model, on the other hand, are very similar to our best-fit LGI models and provide as good fits to the CJ-F data, with the important exception that

  1. Module Configuration

    DOEpatents

    Oweis, Salah; D'Ussel, Louis; Chagnon, Guy; Zuhowski, Michael; Sack, Tim; Laucournet, Gaullume; Jackson, Edward J.

    2002-06-04

    A stand alone battery module including: (a) a mechanical configuration; (b) a thermal management configuration; (c) an electrical connection configuration; and (d) an electronics configuration. Such a module is fully interchangeable in a battery pack assembly, mechanically, from the thermal management point of view, and electrically. With the same hardware, the module can accommodate different cell sizes and, therefore, can easily have different capacities. The module structure is designed to accommodate the electronics monitoring, protection, and printed wiring assembly boards (PWAs), as well as to allow airflow through the module. A plurality of modules may easily be connected together to form a battery pack. The parts of the module are designed to facilitate their manufacture and assembly.

  2. Eliminating Bias

    EPA Pesticide Factsheets

    Learn how to eliminate bias from monitoring systems by instituting appropriate installation, operation, and quality assurance procedures. Provides links to download An Operator's Guide to Eliminating Bias in CEM Systems.

  3. Volunteer Bias in Recruitment, Retention, and Blood Sample Donation in a Randomised Controlled Trial Involving Mothers and Their Children at Six Months and Two Years: A Longitudinal Analysis

    PubMed Central

    Jordan, Sue; Watkins, Alan; Storey, Mel; Allen, Steven J.; Brooks, Caroline J.; Garaiova, Iveta; Heaven, Martin L.; Jones, Ruth; Plummer, Sue F.; Russell, Ian T.; Thornton, Catherine A.; Morgan, Gareth

    2013-01-01

    Background The vulnerability of clinical trials to volunteer bias is under-reported. Volunteer bias is systematic error due to differences between those who choose to participate in studies and those who do not. Methods and Results This paper extends the applications of the concept of volunteer bias by using data from a trial of probiotic supplementation for childhood atopy in healthy dyads to explore 1) differences between a) trial participants and aggregated data from publicly available databases b) participants and non-participants as the trial progressed 2) impact on trial findings of weighting data according to deprivation (Townsend) fifths in the sample and target populations. 1) a) Recruits (n = 454) were less deprived than the target population, matched for area of residence and delivery dates (n = 6,893) (mean [SD] deprivation scores 0.09[4.21] and 0.79[4.08], t = 3.44, df = 511, p<0.001). b) i)As the trial progressed, representation of the most deprived decreased. These participants and smokers were less likely to be retained at 6 months (n = 430[95%]) (OR 0.29,0.13–0.67 and 0.20,0.09–0.46), and 2 years (n = 380[84%]) (aOR 0.68,0.50–0.93 and 0.55,0.28–1.09), and consent to infant blood sample donation (n = 220[48%]) (aOR 0.72,0.57–0.92 and 0.43,0.22–0.83). ii)Mothers interested in probiotics or research or reporting infants’ adverse events or rashes were more likely to attend research clinics and consent to skin-prick testing. Mothers participating to help children were more likely to consent to infant blood sample donation. 2) In one trial outcome, atopic eczema, the intervention had a positive effect only in the over-represented, least deprived group. Here, data weighting attenuated risk reduction from 6.9%(0.9–13.1%) to 4.6%(−1.4–+10.5%), and OR from 0.40(0.18–0.91) to 0.56(0.26–1.21). Other findings were unchanged. Conclusions Potential for volunteer bias intensified during the trial, due to non

  4. Evaluating outcome-correlated recruitment and geographic recruitment bias in a respondent-driven sample of people who inject drugs in Tijuana, Mexico.

    PubMed

    Rudolph, Abby E; Gaines, Tommi L; Lozada, Remedios; Vera, Alicia; Brouwer, Kimberly C

    2014-12-01

    Respondent-driven sampling's (RDS) widespread use and reliance on untested assumptions suggests a need for new exploratory/diagnostic tests. We assessed geographic recruitment bias and outcome-correlated recruitment among 1,048 RDS-recruited people who inject drugs (Tijuana, Mexico). Surveys gathered demographics, drug/sex behaviors, activity locations, and recruiter-recruit pairs. Simulations assessed geographic and network clustering of active syphilis (RPR titers ≥1:8). Gender-specific predicted probabilities were estimated using logistic regression with GEE and robust standard errors. Active syphilis prevalence was 7 % (crude: men = 5.7 % and women = 16.6 %; RDS-adjusted: men = 6.7 % and women = 7.6 %). Syphilis clustered in the Zona Norte, a neighborhood known for drug and sex markets. Network simulations revealed geographic recruitment bias and non-random recruitment by syphilis status. Gender-specific prevalence estimates accounting for clustering were highest among those living/working/injecting/buying drugs in the Zona Norte and directly/indirectly connected to syphilis cases (men: 15.9 %, women: 25.6 %) and lowest among those with neither exposure (men: 3.0 %, women: 6.1 %). Future RDS analyses should assess/account for network and spatial dependencies.

  5. Selection bias from sampling frames: telephone directory and electoral roll compared with door-to-door population census: results from the Blue Mountains Eye Study.

    PubMed

    Smith, W; Mitchell, P; Attebo, K; Leeder, S

    1997-04-01

    Many Australian public health research studies use the telephone directory or the electoral roll as a sampling frame from which to draw study subjects. The sociodemographic, disease-state and risk-factor characteristics of subjects who could be recruited using only the telephone directory or only the electoral roll sampling frames were compared with the characteristics of subjects who would have been missed using only these sampling frames, respectively. In the first phase of the Blue Mountains Eye Study we interviewed and examined 2557 people aged 49 and over living in a defined postcode area, recruited from a door-to-door census. This represented a participation rate of 80.9 per cent and a response rate of 87.9 per cent. The telephone directory was searched for each subject's telephone number and the electoral roll was searched for each subject. Subject characteristics for those who were present in each of these sampling frames were compared with the characteristics of those subjects not included in the sampling frames. The telephone directory listed 2102 (82.2 per cent) of the subjects, and 115 (4.5 per cent) had no telephone connected. The electoral roll contained 2156 (84.3 per cent) of the subjects, and 141 subjects (5.5 per cent) could not be found in either the electoral roll or the telephone directory. Younger subjects, subjects who did not own their own homes and subjects born outside of Australia were significantly less likely to be included in either of these sampling frames. The telephone directory was also more likely to exclude subjects with higher occupational prestige, while the electoral roll was more likely to exclude unmarried persons and males. Researchers using the telephone directory and electoral roll to select subjects for study should be aware of the potential selection bias these sampling frames incur and need to take care when generalising their findings to the wider community.

  6. Service configuration, unit characteristics and variation in intervention rates in a national sample of obstetric units in England: an exploratory analysis

    PubMed Central

    Rowe, Rachel E; Townend, John; Brocklehurst, Peter; Knight, Marian; Macfarlane, Alison; McCourt, Christine; Newburn, Mary; Redshaw, Maggie; Sandall, Jane; Silverton, Louise; Hollowell, Jennifer

    2014-01-01

    Objectives To explore whether service configuration and obstetric unit (OU) characteristics explain variation in OU intervention rates in ‘low-risk’ women. Design Ecological study using funnel plots to explore unit-level variations in adjusted intervention rates and simple linear regression, stratified by parity, to investigate possible associations between unit characteristics/configuration and adjusted intervention rates in planned OU births. Characteristics considered: OU size, presence of an alongside midwifery unit (AMU), proportion of births in the National Health Service (NHS) trust planned in midwifery units or at home and midwifery ‘under’ staffing. Setting 36 OUs in England. Participants ‘Low-risk’ women with a ‘term’ pregnancy planning vaginal birth in a stratified, random sample of 36 OUs. Main outcome measures Adjusted rates of intrapartum caesarean section, instrumental delivery and two composite measures capturing birth without intervention (‘straightforward’ and ‘normal’ birth). Results Funnel plots showed unexplained variation in adjusted intervention rates. In NHS trusts where proportionately more non-OU births were planned, adjusted intrapartum caesarean section rates in the planned OU births were significantly higher (nulliparous: R2=31.8%, coefficient=0.31, p=0.02; multiparous: R2=43.2%, coefficient=0.23, p=0.01), and for multiparous women, rates of ‘straightforward’ (R2=26.3%, coefficient=−0.22, p=0.01) and ‘normal’ birth (R2=17.5%, coefficient=0.24, p=0.01) were lower. The size of the OU (number of births), midwifery ‘under’ staffing levels (the proportion of shifts where there were more women than midwives) and the presence of an AMU were associated with significant variation in some interventions. Conclusions Trusts with greater provision of non-OU intrapartum care may have higher intervention rates in planned ‘low-risk’ OU births, but at a trust level this is likely to be more than offset by lower

  7. Service configuration, unit characteristics and variation in intervention rates in a national sample of obstetric units in England: an exploratory analysis.

    PubMed

    Rowe, Rachel E; Townend, John; Brocklehurst, Peter; Knight, Marian; Macfarlane, Alison; McCourt, Christine; Newburn, Mary; Redshaw, Maggie; Sandall, Jane; Silverton, Louise; Hollowell, Jennifer

    2014-05-29

    To explore whether service configuration and obstetric unit (OU) characteristics explain variation in OU intervention rates in 'low-risk' women. Ecological study using funnel plots to explore unit-level variations in adjusted intervention rates and simple linear regression, stratified by parity, to investigate possible associations between unit characteristics/configuration and adjusted intervention rates in planned OU births. Characteristics considered: OU size, presence of an alongside midwifery unit (AMU), proportion of births in the National Health Service (NHS) trust planned in midwifery units or at home and midwifery 'under' staffing. 36 OUs in England. 'Low-risk' women with a 'term' pregnancy planning vaginal birth in a stratified, random sample of 36 OUs. Adjusted rates of intrapartum caesarean section, instrumental delivery and two composite measures capturing birth without intervention ('straightforward' and 'normal' birth). Funnel plots showed unexplained variation in adjusted intervention rates. In NHS trusts where proportionately more non-OU births were planned, adjusted intrapartum caesarean section rates in the planned OU births were significantly higher (nulliparous: R(2)=31.8%, coefficient=0.31, p=0.02; multiparous: R(2)=43.2%, coefficient=0.23, p=0.01), and for multiparous women, rates of 'straightforward' (R(2)=26.3%, coefficient=-0.22, p=0.01) and 'normal' birth (R(2)=17.5%, coefficient=0.24, p=0.01) were lower. The size of the OU (number of births), midwifery 'under' staffing levels (the proportion of shifts where there were more women than midwives) and the presence of an AMU were associated with significant variation in some interventions. Trusts with greater provision of non-OU intrapartum care may have higher intervention rates in planned 'low-risk' OU births, but at a trust level this is likely to be more than offset by lower intervention rates in planned non-OU births. Further research using high quality data on unit characteristics and

  8. Bias in clinical chemistry.

    PubMed

    Theodorsson, Elvar; Magnusson, Bertil; Leito, Ivo

    2014-01-01

    Clinical chemistry uses automated measurement techniques and medical knowledge in the interest of patients and healthy subjects. Automation has reduced repeatability and day-to-day variation considerably. Bias has been reduced to a lesser extent by reference measurement systems. It is vital to minimize clinically important bias, in particular bias within conglomerates of laboratories that measure samples from the same patients. Small and variable bias components will over time show random error properties and conventional random-error based methods for calculating measurement uncertainty can then be applied. The present overview of bias presents the general principles of error and uncertainty concepts, terminology and analysis, and suggests methods to minimize bias and measurement uncertainty in the interest of healthcare.

  9. Mapping transmission risk of Lassa fever in West Africa: the importance of quality control, sampling bias, and error weighting.

    PubMed

    Peterson, A Townsend; Moses, Lina M; Bausch, Daniel G

    2014-01-01

    Lassa fever is a disease that has been reported from sites across West Africa; it is caused by an arenavirus that is hosted by the rodent M. natalensis. Although it is confined to West Africa, and has been documented in detail in some well-studied areas, the details of the distribution of risk of Lassa virus infection remain poorly known at the level of the broader region. In this paper, we explored the effects of certainty of diagnosis, oversampling in well-studied region, and error balance on results of mapping exercises. Each of the three factors assessed in this study had clear and consistent influences on model results, overestimating risk in southern, humid zones in West Africa, and underestimating risk in drier and more northern areas. The final, adjusted risk map indicates broad risk areas across much of West Africa. Although risk maps are increasingly easy to develop from disease occurrence data and raster data sets summarizing aspects of environments and landscapes, this process is highly sensitive to issues of data quality, sampling design, and design of analysis, with macrogeographic implications of each of these issues and the potential for misrepresenting real patterns of risk.

  10. Intergroup bias.

    PubMed

    Hewstone, Miles; Rubin, Mark; Willis, Hazel

    2002-01-01

    This chapter reviews the extensive literature on bias in favor of in-groups at the expense of out-groups. We focus on five issues and identify areas for future research: (a) measurement and conceptual issues (especially in-group favoritism vs. out-group derogation, and explicit vs. implicit measures of bias); (b) modern theories of bias highlighting motivational explanations (social identity, optimal distinctiveness, uncertainty reduction, social dominance, terror management); (c) key moderators of bias, especially those that exacerbate bias (identification, group size, status and power, threat, positive-negative asymmetry, personality and individual differences); (d) reduction of bias (individual vs. intergroup approaches, especially models of social categorization); and (e) the link between intergroup bias and more corrosive forms of social hostility.

  11. Investigating dimensionality and measurement bias of DSM-5 Alcohol Use Disorder in a representative sample of the largest metropolitan area in South America

    PubMed Central

    Castaldelli-Maia, João Mauricio; Wang, Yuan-Pang; Borges, Guilherme; Silveira, Camila M.; Siu, Erica R.; Viana, Maria C.; Andrade, Arthur G.; Martins, Silvia S.; Andrade, Laura H.

    2016-01-01

    Background Given the recent launch of a new diagnostic classification (DSM-5) for alcohol use disorders (AUD), we aimed to investigate its dimensionality and possible measurement bias in a non-U.S. sample. Methods The current analyses were restricted to 948 subjects who endorsed drinking at least 1 drink per week in the past year from a sample of 5,037 individuals. Data came from São Paulo Megacity Project (which is part of World Mental Health Surveys) collected between 2005–2007. First, exploratory factor analysis (EFA) was carried out to test for the best dimensional structure for DSM-5-AUD criteria. Then, item response theory (IRT) was used to investigate the severity and discrimination properties of each criterion of DSM-5-AUD. Finally, differential criteria functioning (DCF) were investigated by sociodemographics (income, gender, age, employment status, marital status and education). All analyses were performed in Mplus software taking into account complex survey design features. Results The best EFA model was a one-dimensional model. IRT results showed that the criteria “Time Spent” and “Given Up” have the highest discrimination and severity properties, while the criterion “Larger/Longer” had the lowest value of severity, but an average value of discrimination. Only female gender had DCF both at criterion- and factor-level, rendering measurement bias. Conclusion This study reinforces the existence of a DSM-5-AUD continuum in the largest metropolitan area of South America, including subgroups that had previously higher rates of alcohol use (lower educational/income levels). Lower DSM-5-AUD scores were found in women. PMID:26002376

  12. STELLAR POPULATIONS FROM SPECTROSCOPY OF A LARGE SAMPLE OF QUIESCENT GALAXIES AT Z > 1: MEASURING THE CONTRIBUTION OF PROGENITOR BIAS TO EARLY SIZE GROWTH

    SciTech Connect

    Belli, Sirio; Ellis, Richard S.; Newman, Andrew B.

    2015-02-01

    We analyze the stellar populations of a sample of 62 massive (log M {sub *}/M {sub ☉} > 10.7) galaxies in the redshift range 1 < z < 1.6, with the main goal of investigating the role of recent quenching in the size growth of quiescent galaxies. We demonstrate that our sample is not biased toward bright, compact, or young galaxies, and thus is representative of the overall quiescent population. Our high signal-to-noise ratio Keck/LRIS spectra probe the rest-frame Balmer break region that contains important absorption line diagnostics of recent star formation activity. We obtain improved measures of the various stellar population parameters, including the star formation timescale τ, age, and dust extinction, by fitting templates jointly to both our spectroscopic and broadband photometric data. We identify which quiescent galaxies were recently quenched and backtrack their individual evolving trajectories on the UVJ color-color plane finding evidence for two distinct quenching routes. By using sizes measured in the previous paper of this series, we confirm that the largest galaxies are indeed among the youngest at a given redshift. This is consistent with some contribution to the apparent growth from recent arrivals, an effect often called progenitor bias. However, we calculate that recently quenched objects can only be responsible for about half the increase in average size of quiescent galaxies over a 1.5 Gyr period, corresponding to the redshift interval 1.25 < z < 2. The remainder of the observed size evolution arises from a genuine growth of long-standing quiescent galaxies.

  13. Matrix effects on the accuracy of Pb isotope ratio measurement by MC-ICP-MS: variation of instrumental mass bias with sampling depth in the plasma

    NASA Astrophysics Data System (ADS)

    Barling, J.; Weis, D. A.

    2009-12-01

    Accuracy and precision achieved for Pb isotope ratio measurements by MC-ICP-MS are still significantly lower than those achieved for analysis of internally normalized elements (e.g. Hf). External normalization of the instrumental mass bias of Pb (f(Pb)) using f(Tl) requires that f(Pb) and f(Tl) respond identically in the presence of matrix, otherwise inaccuracies are introduced into the data. Addition of a common Mg matrix in an effort to matrix match samples and standards has been shown to improve the precision and accuracy of MC-ICP-MS Pb data (Barling & Weis, 2008). In order to better understand the effect of matrix on plasma conditions, we have measured Pb and Tl isotope ratios and intensities of Pb, Tl and Ar and matrix species over a range of sampling depths in the plasma. Paired matrix-free and matrix-bearing depth traverses were made for a number of matrix elements. For all traverses f(Pb) and f(Tl) decreased with increasing sampling depth. However, relative shifts between paired matrix-bearing and matrix-free traverses vary with element. For Mg, Cs and Sb trends are parallel to the matrix-free trends: for Mg (intermediate ionization potential -IP) and Cs (low IP) the matrix-bearing traverses have low f, whereas the Sb (high IP) trend has high f. By comparison with the matrix-free traverses, in the presence of Mg and Cs matrix, Pb and Tl show fractionation equivalent to a greater sampling depth in matrix-free plasma. This shift in fractionation may be related to enhanced electron-impact ionization due to extra electrons supplied by the matrix element. In contrast to Cs and Sb, Ba and Ce (two elements with low 2nd IP) form significant amounts of polyatomic species and doubly charged ions in the plasma. These matrices result in high f trends that are not parallel to matrix-free trends. For Ba the difference between matrix-bearing and matrix free trends decreases with increasing sampling depth while the reverse is true for Ce. This may relate to the formation

  14. LOW-RESOLUTION SPECTROSCOPY OF GAMMA-RAY BURST OPTICAL AFTERGLOWS: BIASES IN THE SWIFT SAMPLE AND CHARACTERIZATION OF THE ABSORBERS

    SciTech Connect

    Fynbo, J. P. U.; Malesani, D.; Vreeswijk, P. M.; Hjorth, J.; Sollerman, J.; Thoene, C. C.; Jakobsson, P.; Bjoernsson, G.; De Cia, A.; Prochaska, J. X.; Nardini, M.; Chen, H.-W.; Bloom, J. S.; Castro-Tirado, A. J.; Gorosabel, J.; Christensen, L.; Fruchter, A. S.

    2009-12-01

    We present a sample of 77 optical afterglows (OAs) of Swift detected gamma-ray bursts (GRBs) for which spectroscopic follow-up observations have been secured. Our first objective is to measure the redshifts of the bursts. For the majority (90%) of the afterglows, the redshifts have been determined from the spectra. We provide line lists and equivalent widths (EWs) for all detected lines redward of Ly{alpha} covered by the spectra. In addition to the GRB absorption systems, these lists include line strengths for a total of 33 intervening absorption systems. We discuss to what extent the current sample of Swift bursts with OA spectroscopy is a biased subsample of all Swift detected GRBs. For that purpose we define an X-ray-selected statistical sample of Swift bursts with optimal conditions for ground-based follow-up from the period 2005 March to 2008 September; 146 bursts fulfill our sample criteria. We derive the redshift distribution for the statistical (X-ray selected) sample and conclude that less than 18% of Swift bursts can be at z > 7. We compare the high-energy properties (e.g., {gamma}-ray (15-350 keV) fluence and duration, X-ray flux, and excess absorption) for three subsamples of bursts in the statistical sample: (1) bursts with redshifts measured from OA spectroscopy; (2) bursts with detected optical and/or near-IR afterglow, but no afterglow-based redshift; and (3) bursts with no detection of the OA. The bursts in group (1) have slightly higher {gamma}-ray fluences and higher X-ray fluxes and significantly less excess X-ray absorption than bursts in the other two groups. In addition, the fractions of dark bursts, defined as bursts with an optical to X-ray slope {beta}{sub OX} < 0.5, is 14% in group (1), 38% in group (2), and >39% in group (3). For the full sample, the dark burst fraction is constrained to be in the range 25%-42%. From this we conclude that the sample of GRBs with OA spectroscopy is not representative for all Swift bursts, most likely due

  15. Angular Dependence of Exchange Bias and Magnetization Reversal Controlled by Electric-Field-Induced Competing Anisotropies.

    PubMed

    Chen, Aitian; Zhao, Yonggang; Li, Peisen; Zhang, Xu; Peng, Renci; Huang, Haoliang; Zou, Lvkuan; Zheng, Xiaoli; Zhang, Sen; Miao, Peixian; Lu, Yalin; Cai, Jianwang; Nan, Ce-Wen

    2016-01-13

    The combination of exchange-biased systems and ferroelectric materials offers a simple and effective way to investigate the angular dependence of exchange bias using one sample with electric-field-induced competing anisotropies. A reversible electric-field-controlled magnetization reversal at zero magnetic field is also realized through optimizing the anisotropy configuration, holding promising applications for ultralow power magnetoelectric devices. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Tailoring the magnetization reversal of elliptical dots using exchange bias.

    SciTech Connect

    Sort, J.; Buchanan, K. S.; Pearson, J. E.; Hoffmann, A.; Menendez, E.; Salazar-Alvarez, G.; Baro, M. D.; Miron, M.; Rodamcq, B.; Dieny, B.; ICREA; Univ. Autonoma of Barcelona; Insti. Catala de Nanotecnologia; SPINTEC

    2008-01-01

    Exchange bias effects have been studied in elliptical dots composed of ferromagnetic Ni{sub 80}Fe{sub 20}-antiferromagnetic Ir{sub 20}Mn{sub 80} bilayers. The magnetization reversal mechanisms and magnetic configurations have been investigated by magneto-optic Kerr effect and magnetic force microscopy. Although the obtained bias fields in these dots are relatively small, the magnetization reversal is found to be influenced by the ferromagnetic-antiferromagnetic coupling. Namely, for some off-axis angles of measurement, the magnetization reversal mechanism of the Ni{sub 80}Fe{sub 20}-Ir{sub 20}Mn{sub 80} ellipses depends on whether exchange bias is induced along the minor or major axis of the ellipses. Hence, exchange bias is shown to be an effective means for tailoring the magnetization reversal of elliptical dots after sample fabrication.

  17. Study of biological communities subject to imperfect detection: Bias and precision of community N-mixture abundance models in small-sample situations

    USGS Publications Warehouse

    Yamaura, Yuichi; Kery, Marc; Royle, Andy

    2016-01-01

    Community N-mixture abundance models for replicated counts provide a powerful and novel framework for drawing inferences related to species abundance within communities subject to imperfect detection. To assess the performance of these models, and to compare them to related community occupancy models in situations with marginal information, we used simulation to examine the effects of mean abundance (λ¯: 0.1, 0.5, 1, 5), detection probability (p¯: 0.1, 0.2, 0.5), and number of sampling sites (n site : 10, 20, 40) and visits (n visit : 2, 3, 4) on the bias and precision of species-level parameters (mean abundance and covariate effect) and a community-level parameter (species richness). Bias and imprecision of estimates decreased when any of the four variables (λ¯, p¯, n site , n visit ) increased. Detection probability p¯ was most important for the estimates of mean abundance, while λ¯ was most influential for covariate effect and species richness estimates. For all parameters, increasing n site was more beneficial than increasing n visit . Minimal conditions for obtaining adequate performance of community abundance models were n site  ≥ 20, p¯ ≥ 0.2, and λ¯ ≥ 0.5. At lower abundance, the performance of community abundance and community occupancy models as species richness estimators were comparable. We then used additive partitioning analysis to reveal that raw species counts can overestimate β diversity both of species richness and the Shannon index, while community abundance models yielded better estimates. Community N-mixture abundance models thus have great potential for use with community ecology or conservation applications provided that replicated counts are available.

  18. Investigating dimensionality and measurement bias of DSM-5 alcohol use disorder in a representative sample of the largest metropolitan area in South America.

    PubMed

    Castaldelli-Maia, João Mauricio; Wang, Yuan-Pang; Borges, Guilherme; Silveira, Camila M; Siu, Erica R; Viana, Maria C; Andrade, Arthur G; Martins, Silvia S; Andrade, Laura H

    2015-07-01

    Given the recent launch of a new diagnostic classification (DSM-5) for alcohol use disorders (AUD), we aimed to investigate its dimensionality and possible measurement bias in a non-U.S. The current analyses were restricted to 948 subjects who endorsed drinking at least one drink per week in the past year from a sample of 5037 individuals. Data came from São Paulo Megacity Project (which is part of World Mental Health Surveys) collected between 2005 and 2007. First, exploratory factor analysis (EFA) was carried out to test for the best dimensional structure for DSM-5-AUD criteria. Then, item response theory (IRT) was used to investigate the severity and discrimination properties of each criterion of DSM-5-AUD. Finally, differential criterion functioning (DCF) were investigated by socio-demographics (income, gender, age, employment status, marital status and education). All analyses were performed in Mplus software taking into account complex survey design features. The best EFA model was a one-dimensional model. IRT results showed that the criteria "Time Spent" and "Given Up" have the highest discrimination and severity properties, while the criterion "Larger/Longer" had the lowest value of severity, but an average value of discrimination. Only female gender had DCF both at criterion- and factor-level, rendering measurement bias. This study reinforces the existence of a DSM-5-AUD continuum in the largest metropolitan area of South America, including subgroups that had previously higher rates of alcohol use (lower educational/income levels). Lower DSM-5-AUD scores were found in women. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  19. Investigation of the UK37' vs. SST relationship for Atlantic Ocean suspended particulate alkenones: An alternative regression model and discussion of possible sampling bias

    NASA Astrophysics Data System (ADS)

    Gould, Jessica; Kienast, Markus; Dowd, Michael

    2017-05-01

    Alkenone unsaturation, expressed as the UK37' index, is closely related to growth temperature of prymnesiophytes, thus providing a reliable proxy to infer past sea surface temperatures (SSTs). Here we address two lingering uncertainties related to this SST proxy. First, calibration models developed for core-top sediments and those developed for surface suspended particulates organic material (SPOM) show systematic offsets, raising concerns regarding the transfer of the primary signal into the sedimentary record. Second, questions remain regarding changes in slope of the UK37' vs. growth temperature relationship at the temperature extremes. Based on (re)analysis of 31 new and 394 previously published SPOM UK37' data from the Atlantic Ocean, a new regression model to relate UK37' to SST is introduced; the Richards curve (Richards, 1959). This non-linear regression model provides a robust calibration of the UK37' vs. SST relationship for Atlantic SPOM samples and uniquely accounts for both the fact that the UK37' index is a proportion, and so must lie between 0 and 1, as well as for the observed reduction in slope at the warm and cold ends of the temperature range. As with prior fits of SPOM UK37' vs. SST, the Richards model is offset from traditional regression models of sedimentary UK37' vs. SST. We posit that (some of) this offset can be attributed to the seasonally and depth biased sampling of SPOM material.

  20. Active Use of Electronic Health Records (EHRs) and Personal Health Records (PHRs) for Epidemiologic Research: Sample Representativeness and Nonresponse Bias in a Study of Women During Pregnancy.

    PubMed

    Bower, Julie K; Bollinger, Claire E; Foraker, Randi E; Hood, Darryl B; Shoben, Abigail B; Lai, Albert M

    2017-01-01

    With the growing use of electronic medical records, electronic health records (EHRs), and personal health records (PHRs) for health care delivery, new opportunities have arisen for population health researchers. Our objective was to characterize PHR users and examine sample representativeness and nonresponse bias in a study of pregnant women recruited via the PHR. Demographic characteristics were examined for PHR users and nonusers. Enrolled study participants (responders, n=187) were then compared with nonresponders and a representative sample of the target population. PHR patient portal users (34 percent of eligible persons) were older and more likely to be White, have private health insurance, and develop gestational diabetes than nonusers. Of eligible persons (all PHR users), 11 percent (187/1,713) completed a self-administered PHR based questionnaire. Participants in the research study were more likely to be non-Hispanic White (90 percent versus 79 percent) and married (85 percent versus 77 percent), and were less likely to be Non-Hispanic Black (3 percent versus 12 percent) or Hispanic (3 percent versus 6 percent). Responders and nonresponders were similar regarding age distribution, employment status, and health insurance status. Demographic characteristics were similar between responders and nonresponders. Demographic characteristics of the study population differed from the general population, consistent with patterns seen in traditional population-based studies. The PHR may be an efficient method for recruiting and conducting observational research with additional benefits of efficiency and cost-cost-effectiveness.

  1. Selection bias in dynamically-measured super-massive black hole samples: dynamical masses and dependence on Sérsic index

    NASA Astrophysics Data System (ADS)

    Shankar, Francesco; Bernardi, Mariangela; Sheth, Ravi K.

    2017-01-01

    We extend the comparison between the set of local galaxies having dynamically measured black holes with galaxies in the Sloan Digital Sky Survey (SDSS). We first show that the most up-to-date local black hole samples of early-type galaxies with measurements of effective radii, luminosities, and Sérsic indices of the bulges of their host galaxies, have dynamical mass and Sérsic index distributions consistent with those of SDSS early-type galaxies of similar bulge stellar mass. The host galaxies of local black hole samples thus do not appear structurally different from SDSS galaxies, sharing similar dynamical masses, light profiles and light distributions. Analysis of the residuals reveals that velocity dispersion is more fundamental than Sérsic index nsph in the scaling relations between black holes and galaxies. Indeed, residuals with nsph could be ascribed to the (weak) correlation with bulge mass or even velocity dispersion. Finally, targetted Monte Carlo simulations that include the effects of the sphere of influence of the black hole, and tuned to reproduce the observed residuals and scaling relations in terms of velocity dispersion and stellar mass, show that, at least for galaxies with Mbulge ≳ 1010 M⊙ and nsph ≳ 5, the observed mean black hole mass at fixed Sérsic index is biased significantly higher than the intrinsic value.

  2. Active Use of Electronic Health Records (EHRs) and Personal Health Records (PHRs) for Epidemiologic Research: Sample Representativeness and Nonresponse Bias in a Study of Women During Pregnancy

    PubMed Central

    Bower, Julie K; Bollinger, Claire E.; Foraker, Randi E.; Hood, Darryl B.; Shoben, Abigail B.; Lai, Albert M.

    2017-01-01

    Introduction: With the growing use of electronic medical records, electronic health records (EHRs), and personal health records (PHRs) for health care delivery, new opportunities have arisen for population health researchers. Our objective was to characterize PHR users and examine sample representativeness and nonresponse bias in a study of pregnant women recruited via the PHR. Design: Demographic characteristics were examined for PHR users and nonusers. Enrolled study participants (responders, n=187) were then compared with nonresponders and a representative sample of the target population. Results: PHR patient portal users (34 percent of eligible persons) were older and more likely to be White, have private health insurance, and develop gestational diabetes than nonusers. Of eligible persons (all PHR users), 11 percent (187/1,713) completed a self-administered PHR based questionnaire. Participants in the research study were more likely to be non-Hispanic White (90 percent versus 79 percent) and married (85 percent versus 77 percent), and were less likely to be Non-Hispanic Black (3 percent versus 12 percent) or Hispanic (3 percent versus 6 percent). Responders and nonresponders were similar regarding age distribution, employment status, and health insurance status. Demographic characteristics were similar between responders and nonresponders. Discussion: Demographic characteristics of the study population differed from the general population, consistent with patterns seen in traditional population-based studies. The PHR may be an efficient method for recruiting and conducting observational research with additional benefits of efficiency and cost-cost-effectiveness. PMID:28303255

  3. Reducing the Impact of Sampling Bias in NASA MODIS and VIIRS Level 3 Satellite Derived IR SST Observations over the Arctic

    NASA Astrophysics Data System (ADS)

    Minnett, P. J.; Liu, Y.; Kilpatrick, K. A.

    2016-12-01

    Sea-surface temperature (SST) measurements by satellites in the northern hemisphere high latitudes confront several difficulties. Year-round prevalent clouds, effects near ice edges, and the relative small difference between SST and low-level cloud temperatures lead to a significant loss of infrared observations regardless of the more frequent polar satellite overpasses. Recent research (Liu and Minnett, 2016) identified sampling issues in the Level 3 NASA MODIS SST products when 4km observations are aggregated into global grids at different time and space scales, particularly in the Arctic, where a binary decision cloud mask designed for global data is often overly conservative at high latitudes and results in many gaps and missing data. This under sampling of some Arctic regions results in a warm bias in Level 3 products, likely a result of warmer surface temperature, more distant from the ice edge, being identified more frequently as cloud free. Here we present an improved method for cloud detection in the Arctic using a majority vote from an ensemble of four classifiers trained based on an Alternative Decision Tree (ADT) algorithm (Freund and Mason 1999, Pfahringer et. al. 2001). This new cloud classifier increases sampling of clear pixel by 50% in several regions and generally produces cooler monthly average SST fields in the ice-free Arctic, while still retaining the same error characteristics at 1km resolution relative to in situ observations. SST time series of 12 years of MODIS (Aqua and Terra) and more recently VIIRS sensors are compared and the improvements in errors and uncertainties resulting from better cloud screening for Level 3 gridded products are assessed and summarized.

  4. Demographic characteristics do not decrease the utility of depressive symptoms assessments: Examining the practical impact of item bias in four heterogeneous samples of older adults

    PubMed Central

    Dmitrieva, Natalia O.; Fyffe, Denise; Mukherjee, Shubhabrata; Fieo, Robert; Zahodne, Laura B.; Hamilton, Jamie; Potter, Guy G.; Manly, Jennifer J.; Romero, Heather R.; Mungas, Dan; Gibbons, Laura E.

    2014-01-01

    Objective Previous studies have identified differential item function (DIF) in depressive symptoms measures, but the impact of DIF has been rarely reported. Given the critical importance of depressive symptoms assessment among older adults, we examined whether DIF due to demographic characteristics resulted in salient score changes in commonly used measures. Methods Four longitudinal studies of cognitive aging provided a sample size of 3,754 older adults, and included individuals both with and without a clinical diagnosis of major depression. Each study administered at least one of the following measures: the Center for Epidemiologic Studies Depression scale (CES-D; 20-item ordinal response or 10-item dichotomous response versions), the Geriatric Depression Scale (GDS), and the Montgomery-Åsberg Depression Rating Scale (MADRS). Hybrid logistic regression-item response theory methods were used to examine the presence and impact of DIF due to age, sex, race/ethnicity, and years of education on the depressive symptoms items. Results Although statistically significant DIF due to demographic factors was present on several items, its cumulative impact on depressive symptoms scores was practically negligible. Conclusions The findings support substantive meaningfulness of previously reported demographic differences in depressive symptoms among older adults, showing that these individual differences were unlikely to have resulted from item bias attributable to demographic characteristics we examined. PMID:24737612

  5. Demographic characteristics do not decrease the utility of depressive symptoms assessments: examining the practical impact of item bias in four heterogeneous samples of older adults.

    PubMed

    Dmitrieva, Natalia O; Fyffe, Denise; Mukherjee, Shubhabrata; Fieo, Robert; Zahodne, Laura B; Hamilton, Jamie; Potter, Guy G; Manly, Jennifer J; Romero, Heather R; Mungas, Dan; Gibbons, Laura E

    2015-01-01

    Previous studies have identified differential item function (DIF) in depressive symptoms measures, but the impact of DIF has been rarely reported. Given the critical importance of depressive symptoms assessment among older adults, we examined whether DIF due to demographic characteristics resulted in salient score changes in commonly used measures. Four longitudinal studies of cognitive aging provided a sample size of 3754 older adults and included individuals both with and without a clinical diagnosis of major depression. Each study administered at least one of the following measures: the Center for Epidemiologic Studies Depression scale (20-item ordinal response or 10-item dichotomous response versions), the Geriatric Depression Scale, and the Montgomery-Åsberg Depression Rating Scale. Hybrid logistic regression-item response theory methods were used to examine the presence and impact of DIF due to age, sex, race/ethnicity, and years of education on the depressive symptoms items. Although statistically significant DIF due to demographic factors was present on several items, its cumulative impact on depressive symptoms scores was practically negligible. The findings support substantive meaningfulness of previously reported demographic differences in depressive symptoms among older adults, showing that these individual differences were unlikely to have resulted from item bias attributable to demographic characteristics we examined. Copyright © 2014 John Wiley & Sons, Ltd.

  6. The scale-of-choice effect and how estimates of assortative mating in the wild can be biased due to heterogeneous samples.

    PubMed

    Rolán-Alvarez, Emilio; Carvajal-Rodríguez, Antonio; de Coo, Alicia; Cortés, Beatriz; Estévez, Daniel; Ferreira, Mar; González, Rubén; Briscoe, Adriana D

    2015-07-01

    The mode in which sexual organisms choose mates is a key evolutionary process, as it can have a profound impact on fitness and speciation. One way to study mate choice in the wild is by measuring trait correlation between mates. Positive assortative mating is inferred when individuals of a mating pair display traits that are more similar than those expected under random mating while negative assortative mating is the opposite. A recent review of 1134 trait correlations found that positive estimates of assortative mating were more frequent and larger in magnitude than negative estimates. Here, we describe the scale-of-choice effect (SCE), which occurs when mate choice exists at a smaller scale than that of the investigator's sampling, while simultaneously the trait is heterogeneously distributed at the true scale-of-choice. We demonstrate the SCE by Monte Carlo simulations and estimate it in two organisms showing positive (Littorina saxatilis) and negative (L. fabalis) assortative mating. Our results show that both positive and negative estimates are biased by the SCE by different magnitudes, typically toward positive values. Therefore, the low frequency of negative assortative mating observed in the literature may be due to the SCE's impact on correlation estimates, which demands new experimental evaluation.

  7. Exploring the sensitivity of the Personality Assessment Inventory symptom validity tests in detecting response bias in a mixed neuropsychological outpatient sample.

    PubMed

    Gaasedelen, Owen J; Whiteside, Douglas M; Basso, Michael

    2017-07-01

    Few studies have evaluated the symptom validity tests (SVTs) within the Personality Assessment Inventory (PAI) in a neuropsychological assessment context. Accordingly, the present study explored the accuracy of PAI SVTs in identifying exaggerated cognitive dysfunction in a mixed sample of outpatients referred for neuropsychological assessment. Participants who failed two or more Performance Validity Tests (PVTs) were classified as having exaggerated cognitive dysfunction (n = 49). Their responses on PAI SVTs were compared to examinees who did not fail PVTs (n = 257). Multivariate analysis of variance indicated the Negative Impression Management (NIM) scale most strongly discriminated between those with exaggerated cognitive dysfunction from honest responders (Cohen's d = .58). Nonetheless, its classification accuracy was low (area under the curve [AUC] = .65). A k-means cluster analysis and a subsequent multinomial logistic regression indicated evidence for two distinct groups of exaggerators. In particular, one group seemed to exaggerate symptoms, whereas another presented in a defensive manner, implying that individuals with positive and NIM biases on the PAI were apt to display invalid performance on PVTs. Findings indicated that exaggerated cognitive dysfunction tends to be present when NIM is very high and that evidence exists for a defensive response style on the PAI in the context of PVT failure.

  8. Metalloregulator CueR biases RNA polymerase's kinetic sampling of dead-end or open complex to repress or activate transcription.

    PubMed

    Martell, Danya J; Joshi, Chandra P; Gaballa, Ahmed; Santiago, Ace George; Chen, Tai-Yen; Jung, Won; Helmann, John D; Chen, Peng

    2015-11-03

    Metalloregulators respond to metal ions to regulate transcription of metal homeostasis genes. MerR-family metalloregulators act on σ(70)-dependent suboptimal promoters and operate via a unique DNA distortion mechanism in which both the apo and holo forms of the regulators bind tightly to their operator sequence, distorting DNA structure and leading to transcription repression or activation, respectively. It remains unclear how these metalloregulator-DNA interactions are coupled dynamically to RNA polymerase (RNAP) interactions with DNA for transcription regulation. Using single-molecule FRET, we study how the copper efflux regulator (CueR)--a Cu(+)-responsive MerR-family metalloregulator--modulates RNAP interactions with CueR's cognate suboptimal promoter PcopA, and how RNAP affects CueR-PcopA interactions. We find that RNAP can form two noninterconverting complexes at PcopA in the absence of nucleotides: a dead-end complex and an open complex, constituting a branched interaction pathway that is distinct from the linear pathway prevalent for transcription initiation at optimal promoters. Capitalizing on this branched pathway, CueR operates via a "biased sampling" instead of "dynamic equilibrium shifting" mechanism in regulating transcription initiation; it modulates RNAP's binding-unbinding kinetics, without allowing interconversions between the dead-end and open complexes. Instead, the apo-repressor form reinforces the dominance of the dead-end complex to repress transcription, and the holo-activator form shifts the interactions toward the open complex to activate transcription. RNAP, in turn, locks CueR binding at PcopA into its specific binding mode, likely helping amplify the differences between apo- and holo-CueR in imposing DNA structural changes. Therefore, RNAP and CueR work synergistically in regulating transcription.

  9. The impact of non-response bias due to sampling in public health studies: A comparison of voluntary versus mandatory recruitment in a Dutch national survey on adolescent health.

    PubMed

    Cheung, Kei Long; Ten Klooster, Peter M; Smit, Cees; de Vries, Hein; Pieterse, Marcel E

    2017-03-23

    In public health monitoring of young people it is critical to understand the effects of selective non-response, in particular when a controversial topic is involved like substance abuse or sexual behaviour. Research that is dependent upon voluntary subject participation is particularly vulnerable to sampling bias. As respondents whose participation is hardest to elicit on a voluntary basis are also more likely to report risk behaviour, this potentially leads to underestimation of risk factor prevalence. Inviting adolescents to participate in a home-sent postal survey is a typical voluntary recruitment strategy with high non-response, as opposed to mandatory participation during school time. This study examines the extent to which prevalence estimates of adolescent health-related characteristics are biased due to different sampling methods, and whether this also biases within-subject analyses. Cross-sectional datasets collected in 2011 in Twente and IJsselland, two similar and adjacent regions in the Netherlands, were used. In total, 9360 youngsters in a mandatory sample (Twente) and 1952 youngsters in a voluntary sample (IJsselland) participated in the study. To test whether the samples differed on health-related variables, we conducted both univariate and multivariable logistic regression analyses controlling for any demographic difference between the samples. Additional multivariable logistic regressions were conducted to examine moderating effects of sampling method on associations between health-related variables. As expected, females, older individuals, as well as individuals with higher education levels, were over-represented in the voluntary sample, compared to the mandatory sample. Respondents in the voluntary sample tended to smoke less, consume less alcohol (ever, lifetime, and past four weeks), have better mental health, have better subjective health status, have more positive school experiences and have less sexual intercourse than respondents in the

  10. Origin and nature of measurement bias in catadioptric parallel goniophotometers.

    PubMed

    Karamata, Boris; Andersen, Marilyne

    2014-05-01

    We briefly categorize and compare parallel goniophotometers, which are instruments capable of simultaneously measuring the far-field distribution of light scattered by a surface or emitted by a source over a large solid angle. Little is known about the accuracy and reliability of an appealing category, the catadioptric parallel goniophotometers (CPGs), which exploit a curved reflector and a lens system. We analyzed the working principle common to all the different design configurations of a CPG and established the specifications implicitly imposed on the lens system. Based on heuristic considerations, we show that the properties of a real (thick) lens system are not fully compatible with these specifications. This causes a bias to the measurements that increases with the acceptance angle of the lens system. Depending on the angular field, the measured sample area can be drastically reduced and shifted relative to the center of the sample. To gain insights into the nature and importance of the measurement bias, it was calculated with our model implemented in MATLAB for the CPG configuration incorporating a lens system with a very large acceptance angle (fisheye lens). Our results demonstrate that, due to the spatio-angular-filtering properties of the fisheye lens, this category of CPGs is so severely biased as to give unusable measurements. In addition, our findings raise the question of the importance of the bias in the other types of CPGs that rely on a lens system with a lower acceptance angle.

  11. New Trends in Magnetic Exchange Bias

    NASA Astrophysics Data System (ADS)

    Mougin, Alexandra; Mangin, Stéphane; Bobo, Jean-Francois; Loidl, Alois

    2005-05-01

    of the constituant layers. The spirit of this topical issue is, for the first time, to gather and survey recent and original developments, both experimental and theoretical, which bring new insights into the physics of exchange bias. It has been planned in relation with an international workshop exclusively devoted to exchange bias, namely IWEBMN’04 (International Workshop on Exchange Bias in Magnetic Nanostructures) that took place in Anglet, in the south west of France, from 16th to 18th September 2004. The conference gathered worldwide researchers in the area, both experimentalists and theoreticians. Several research paths are particularly active in the field of magnetic exchange coupling. The conference, as well as this topical issue, which was also open to contributions from scientists not participating in the conference, has been organized according to the following principles: 1. Epitaxial systems: Since the essential behavior of exchange bias critically depends on the atomic-level chemical and spin structure at the interface between the ferromagnetic and antiferromagnetic components, epitaxial AF/F systems in which the quality of the interface and the crystalline coherence are optimized and well known are ideal candidates for a better understanding of the underlying physics of exchange bias. The dependence of exchange bias on the spin configurations at the interfaces can be accomplished by selecting different crystallographic orientations. The role of interface roughness can also be understood from thin-film systems by changing the growth parameters, and correlations between the interface structure and exchange bias can be made, as reported in this issue. 2. Out-of-plane magnetized systems: While much important work has been devoted to the study of structures with in-plane magnetization, little has been done on the study of exchange bias and exchange coupling in samples with out-of-plane magnetization. Some systems can exhibit either in-plane or out

  12. Enhanced sampling of rare events

    NASA Astrophysics Data System (ADS)

    Melchionna, Simone

    2000-12-01

    We present a method to enhance sampling of a given reaction coordinate by projecting part of the random thermal noise along a preferential direction. The approach is promising to study rough energy landscapes and highly activated barriers that can be overcome by increasing the attempt frequency. Furthermore it allows us to rescale a given reaction coordinate without biasing the configurational properties of the system. A major advantage of the method is its simplicity in the analytical derivation and numerical implementation.

  13. Journal bias or author bias?

    PubMed

    Harris, Ian

    2016-01-01

    I read with interest the comment by Mark Wilson in the Indian Journal of Medical Ethics regarding bias and conflicts of interest in medical journals. Wilson targets one journal (the New England Journal of Medicine: NEJM) and one particular "scandal" to make his point that journals' decisions on publication are biased by commercial conflicts of interest (CoIs). It is interesting that he chooses the NEJM which, by his own admission, had one of the strictest CoI policies and had published widely on this topic. The feeling is that if the NEJM can be guilty, they can all be guilty.

  14. Bias structure to efficiently package a magnetic bubble domain device

    NASA Technical Reports Server (NTRS)

    Chen, Thomas T. (Inventor)

    1978-01-01

    A single, compact bias structure to efficiently package a plurality of magnetic bubble domain device chips having different bias requirements. The vertical magnetic field distribution within the bias structure air gap is selectively controlled by a magnetically soft field adjusting assembly suitably attached within the bias structure. The size and configuration of the field adjusting assembly tailors local field variations within the air gap to correspond with the bias requirements of the bubble domain chips disposed therein.

  15. Robust Biased Brownian Dynamics for Rate Constant Calculation

    PubMed Central

    Zou, Gang; Skeel, Robert D.

    2003-01-01

    A reaction probability is required to calculate the rate constant of a diffusion-dominated reaction. Due to the complicated geometry and potentially high dimension of the reaction probability problem, it is usually solved by a Brownian dynamics simulation, also known as a random walk or path integral method, instead of solving the equivalent partial differential equation by a discretization method. Building on earlier work, this article completes the development of a robust importance sampling algorithm for Brownian dynamics—i.e., biased Brownian dynamics with weight control—to overcome the high energy and entropy barriers in biomolecular association reactions. The biased Brownian dynamics steers sampling by a bias force, and the weight control algorithm controls sampling by a target weight. This algorithm is optimal if the bias force and the target weight are constructed from the solution of the reaction probability problem. In reality, an approximate reaction probability has to be used to construct the bias force and the target weight. Thus, the performance of the algorithm depends on the quality of the approximation. Given here is a method to calculate a good approximation, which is based on the selection of a reaction coordinate and the variational formulation of the reaction probability problem. The numerically approximated reaction probability is shown by computer experiments to give a factor-of-two speedup over the use of a purely heuristic approximation. Also, the fully developed method is compared to unbiased Brownian dynamics. The tests for human superoxide dismutase, Escherichia coli superoxide dismutase, and antisweetener antibody NC6.8, show speedups of 17, 35, and 39, respectively. The test for reactions between two model proteins with orientations shows speedups of 2578 for one set of configurations and 3341 for another set of configurations. PMID:14507681

  16. Size Bias in Galaxy Surveys

    NASA Astrophysics Data System (ADS)

    Schmidt, Fabian; Rozo, Eduardo; Dodelson, Scott; Hui, Lam; Sheldon, Erin

    2009-07-01

    Only certain galaxies are included in surveys: those bright and large enough to be detectable as extended sources. Because gravitational lensing can make galaxies appear both brighter and larger, the presence of foreground inhomogeneities can scatter galaxies across not only magnitude cuts but also size cuts, changing the statistical properties of the resulting catalog. Here we explore this size bias and how it combines with magnification bias to affect galaxy statistics. We demonstrate that photometric galaxy samples from current and upcoming surveys can be even more affected by size bias than by magnification bias.

  17. Sequential biases in accumulating evidence.

    PubMed

    Kulinskaya, Elena; Huggins, Richard; Dogo, Samson Henry

    2016-09-01

    Whilst it is common in clinical trials to use the results of tests at one phase to decide whether to continue to the next phase and to subsequently design the next phase, we show that this can lead to biased results in evidence synthesis. Two new kinds of bias associated with accumulating evidence, termed 'sequential decision bias' and 'sequential design bias', are identified. Both kinds of bias are the result of making decisions on the usefulness of a new study, or its design, based on the previous studies. Sequential decision bias is determined by the correlation between the value of the current estimated effect and the probability of conducting an additional study. Sequential design bias arises from using the estimated value instead of the clinically relevant value of an effect in sample size calculations. We considered both the fixed-effect and the random-effects models of meta-analysis and demonstrated analytically and by simulations that in both settings the problems due to sequential biases are apparent. According to our simulations, the sequential biases increase with increased heterogeneity. Minimisation of sequential biases arises as a new and important research area necessary for successful evidence-based approaches to the development of science. © 2015 The Authors. Research Synthesis Methods Published by John Wiley & Sons Ltd. © 2015 The Authors. Research Synthesis Methods Published by John Wiley & Sons Ltd.

  18. The Effect of Perceived Injustice on Appraisals of Physical Activity: An Examination of the Mediating Role of Attention Bias to Pain in a Chronic Low Back Pain Sample.

    PubMed

    Trost, Zina; Van Ryckeghem, Dimitri; Scott, Whitney; Guck, Adam; Vervoort, Tine

    2016-11-01

    The current study examined the relationship between perceived injustice and attentional bias (AB) toward pain among individuals with chronic low back pain asked to perform and appraise the pain and difficulty of a standardized set of common physical activities. A pictorial dot-probe task assessed AB toward pain stimuli (ie, pain faces cueing pain), after which participants performed the physical tasks. Participants also rated face stimuli in terms of pain, sadness, and anger expression. As hypothesized, perceived injustice was positively associated with AB toward pain stimuli; additionally, perceived injustice and AB were positively associated with appraisals of pain and difficulty. Counter to expectations, AB did not mediate the relationship between perceived injustice and task appraisals, suggesting that AB is insufficient to explain this relationship. Exploratory analyses indicated that participants with higher levels of perceived injustice rated stimulus faces as sadder and angrier; no such differences emerged for pain ratings. To our knowledge, this is the first study to examine the association between perceived injustice and AB toward pain, as well as perceived injustice and in vivo appraisals of common physical activity. Results extend existing literature and suggest that attentional and potential interpretive bias should be considered in future research. This article identifies significant associations between perceived injustice, biased attention to pain, and appraisals of common physical activities among individuals with chronic low back pain. These findings suggest targets for intervention as well as directions for future research regarding individuals with high perceptions of injustice related to pain. Copyright © 2016 American Pain Society. Published by Elsevier Inc. All rights reserved.

  19. Bias modification training can alter approach bias and chocolate consumption.

    PubMed

    Schumacher, Sophie E; Kemps, Eva; Tiggemann, Marika

    2016-01-01

    Recent evidence has demonstrated that bias modification training has potential to reduce cognitive biases for attractive targets and affect health behaviours. The present study investigated whether cognitive bias modification training could be applied to reduce approach bias for chocolate and affect subsequent chocolate consumption. A sample of 120 women (18-27 years) were randomly assigned to an approach-chocolate condition or avoid-chocolate condition, in which they were trained to approach or avoid pictorial chocolate stimuli, respectively. Training had the predicted effect on approach bias, such that participants trained to approach chocolate demonstrated an increased approach bias to chocolate stimuli whereas participants trained to avoid such stimuli showed a reduced bias. Further, participants trained to avoid chocolate ate significantly less of a chocolate muffin in a subsequent taste test than participants trained to approach chocolate. Theoretically, results provide support for the dual process model's conceptualisation of consumption as being driven by implicit processes such as approach bias. In practice, approach bias modification may be a useful component of interventions designed to curb the consumption of unhealthy foods. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Non-local bias contribution to third-order galaxy correlations

    NASA Astrophysics Data System (ADS)

    Bel, J.; Hoffmann, K.; Gaztañaga, E.

    2015-10-01

    We study halo clustering bias with second- and third-order statistics of halo and matter density fields in the Marenostrum Institut de Ciències de l'Espai (MICE) Grand Challenge simulation. We verify that two-point correlations deliver reliable estimates of the linear bias parameters at large scales, while estimations from the variance can be significantly affected by non-linear and possibly non-local contributions to the bias function. Combining three-point auto- and cross-correlations we find, for the first time in configuration space, evidence for the presence of such non-local contributions. These contributions are consistent with predicted second-order non-local effects on the bias functions originating from the dark matter tidal field. Samples of massive haloes show indications of bias (local or non-local) beyond second order. Ignoring non-local bias causes 20-30 and 5-10 per cent overestimation of the linear bias from three-point auto- and cross-correlations, respectively. We study two third-order bias estimators that are not affected by second-order non-local contributions. One is a combination of three-point auto- and cross-correlations. The other is a combination of third-order one- and two-point cumulants. Both methods deliver accurate estimations of the linear bias. Ignoring non-local bias causes higher values of the second-order bias from three-point correlations. Our results demonstrate that third-order statistics can be employed for breaking the growth-bias degeneracy.

  1. Does the requirement of getting active consent from parents in school-based research result in a biased sample? An empirical study.

    PubMed

    Jelsma, Jennifer; Burgess, Theresa; Henley, Lesley

    2012-12-01

    Active parental consent is a requirement that may threaten the validity of including minors in research. This study investigated possible sources of bias between the responses of children whose parents actively consented to their participation in a school-based survey and those of children whose parents were nonresponders. Due to a serious administrative error in a study to examine health-related quality of life (HRQoL), all 514 eligible schoolchildren were tested, although only 177 parents signed consent. After deliberation, the relevant human research ethics committee gave permission to include all results in the analysis. The HRQoL was not different between the groups. Male children returned significantly fewer consent forms (p=.026). More of the nonresponding group reported that their parents "Never had enough time for them" (p=.023). The high nonresponse rate and associations between response and parental interest and gender indicate that some bias may be introduced through the need for active consent, but overall there were no differences in responses to the quality of life questionnaire.

  2. Evaluating outcome-correlated recruitment and geographic recruitment bias in a respondent-driven sample of people who inject drugs in Tijuana, Mexico

    PubMed Central

    Rudolph, Abby E.; Gaines, Tommi L.; Lozada, Remedios; Vera, Alicia; Brouwer, Kimberly C.

    2015-01-01

    Respondent-driven sampling’s (RDS) widespread use and reliance on untested assumptions suggests a need for new exploratory/diagnostic tests. We assessed geographic recruitment bias and outcome-correlated recruitment among 1048 RDS-recruited people who inject drugs (Tijuana, Mexico). Surveys gathered demographics, drug/sex behaviors, activity locations, and recruiter-recruit pairs. Simulations assessed geographic and network clustering of active syphilis (RPR titers≥1:8). Gender-specific predicted probabilities were estimated using logistic regression with GEE and robust standard errors. Active syphilis prevalence was 7% (crude: men=5.7% and women=16.6%; RDS-adjusted: men=6.7% and women=7.6%). Syphilis clustered in the Zona Norte, a neighborhood known for drug and sex markets. Network simulations revealed geographic recruitment bias and non-random recruitment by syphilis status. Gender-specific prevalence estimates accounting for clustering were highest among those living/working/injecting/buying drugs in the Zona Norte and directly/indirectly connected to syphilis cases (men:15.9%, women:25.6%) and lowest among those with neither exposure (men:3.0%, women:6.1%). Future RDS analyses should assess/account for network and spatial dependencies. PMID:24969586

  3. A bias identification and state estimation methodology for nonlinear systems

    NASA Technical Reports Server (NTRS)

    Caglayan, A. K.; Lancraft, R. E.

    1983-01-01

    A computational algorithm for the identification of input and output biases in discrete-time nonlinear stochastic systems is derived by extending the separate bias estimation results for linear systems to the extended Kalman filter formulation. The merits of the approach are illustrated by identifying instrument biases using a terminal configured vehicle simulation.

  4. System and circuitry to provide stable transconductance for biasing

    NASA Technical Reports Server (NTRS)

    Garverick, Steven L. (Inventor); Yu, Xinyu (Inventor)

    2012-01-01

    An amplifier system can include an input amplifier configured to receive an analog input signal and provide an amplified signal corresponding to the analog input signal. A tracking loop is configured to employ delta modulation for tracking the amplified signal, the tracking loop providing a corresponding output signal. A biasing circuit is configured to adjust a bias current to maintain stable transconductance over temperature variations, the biasing circuit providing at least one bias signal for biasing at least one of the input amplifier and the tracking loop, whereby the circuitry receiving the at least one bias signal exhibits stable performance over the temperature variations. In another embodiment the biasing circuit can be utilized in other applications.

  5. Advantages of using a modified orthogonal sampling configuration originally designed for LC-ESI-MS to couple CE and MS for the determination of antioxidant phenolic compounds found in virgin olive oil.

    PubMed

    Nevado, Juan José Berzas; Peñalvo, Gregorio Castañeda; Robledo, Virginia Rodríguez

    2010-07-15

    A ThermoFinnigan sheath liquid flow capillary electrophoresis-mass spectrometry system designed for coupling via a co-axial interface was coupled through an adapted via an alternative, commercially available interface for orthogonal sampling. The affordable, reversible structural alterations made in the commercial LC-MS interface resulted in improved analytical performance. The results of a conventional capillary electrophoresis (CE) method using a commercial co-axial source to determine antioxidant phenolic acids present in virgin olive oil, were compared with those obtained by using a modified orthogonal sampling position. In both cases, separations were done using a 10 mM ammonium acetate/ammonium hydroxide buffer solution at pH 10.0 and a constant applied voltage of 25 kV. The operating variables for the mass spectrometry interface were re-optimized for the modified orthogonal orientation. This allowed the sheath liquid, sheath gas flow rates and capillary voltage to be lowered with respect to the co-axial coupling configuration. In addition, the orthogonal sampling position provided a higher selectivity by effect of ion sampling excluding larger droplets-with an increased momentum along the axis-which were drained through the sink at the bottom of the ion source. Also, the new configuration facilitated sample ionization, improved electrospray stability and led to stronger signals as a result. The new system was validated in terms of precision (repeatability), linearity, and limits of detection and quantification. A comparison of the validation data with the results previously obtained by using a commercial co-axial configuration revealed the adapted orthogonal sampling position to provide better repeatability in both migration times and relative peak areas (<1% and 7% respectively with n=15 replicates), a good linear range (with levels in the microgram-per-litre region) and lower limits of detection-especially for the compounds detected with the lowest

  6. The clustering of galaxies in the completed SDSS-III Baryon Oscillation Spectroscopic Survey: tomographic BAO analysis of DR12 combined sample in configuration space

    NASA Astrophysics Data System (ADS)

    Wang, Yuting; Zhao, Gong-Bo; Chuang, Chia-Hsun; Ross, Ashley J.; Percival, Will J.; Gil-Marín, Héctor; Cuesta, Antonio J.; Kitaura, Francisco-Shu; Rodriguez-Torres, Sergio; Brownstein, Joel R.; Eisenstein, Daniel J.; Ho, Shirley; Kneib, Jean-Paul; Olmstead, Matthew D.; Prada, Francisco; Rossi, Graziano; Sánchez, Ariel G.; Salazar-Albornoz, Salvador; Thomas, Daniel; Tinker, Jeremy; Tojeiro, Rita; Vargas-Magaña, Mariana; Zhu, Fangzhou

    2017-08-01

    We perform a tomographic baryon acoustic oscillations (BAOs) analysis using the two-point galaxy correlation function measured from the combined sample of Baryon Oscillation Spectroscopic Survey Data Release 12 (BOSS DR12), which covers the redshift range of 0.2 < z < 0.75. Upon splitting the sample into multiple overlapping redshift slices to extract the redshift information of galaxy clustering, we obtain a measurement of DA(z)/rd and H(z)rd at nine effective redshifts with the full covariance matrix calibrated using MultiDark-Patchy mock catalogues. Using the reconstructed galaxy catalogues, we obtain the precision of 1.3-2.2 per cent for DA(z)/rd and 2.1-6.0 per cent for H(z)rd. To quantify the gain from the tomographic information, we compare the constraints on the cosmological parameters using our nine-bin BAO measurements, the consensus three-bin BAO and redshift space distortion measurements at three effective redshifts in Alam et al., and the non-tomographic (one-bin) BAO measurement at a single effective redshift. Comparing the nine-bin with one-bin constraint result, it can improve the dark energy Figure of Merit by a factor of 1.24 for the Chevallier-Polarski-Linder parametrization for equation-of-state parameter wDE. The errors of w0 and wa from nine-bin constraints are slightly improved when compared to the three-bin constraint result.

  7. Impact of Substrate Bias on Fixed-Pattern-Noise in Active Pixel Sensor Cells

    NASA Astrophysics Data System (ADS)

    Terauchi, Mamoru

    2007-11-01

    The effect of substrate (body) bias on fixed-pattern-noise (FPN) in active pixel sensor (APS) cells is studied. Through measuring test devices consisting of two metal-oxide-semiconductor field-effect transistors (MOSFETs) connected in series with each of the transistors located in the same well region, it has been revealed that substrate bias, which is inevitably applied in a normal circuit configuration in conventional APS cells, worsens the characteristics fluctuation in source-follower amplifiers in APS cells, leading to FPN that cannot be mitigated by conventional correction methods such as correlated double sampling. In addition it has been confirmed that the current-voltage characteristics of logarithmic converters, each of which is realized using a MOSFET with gate and drain terminals connected together, are also affected by substrate bias, resulting in increased characteristics fluctuation as compared with the case with no substrate bias.

  8. Tailoring the magnetization reversal of elliptical dots using exchange bias (invited)

    NASA Astrophysics Data System (ADS)

    Sort, J.; Buchanan, K. S.; Pearson, J. E.; Hoffmann, A.; Menéndez, E.; Salazar-Alvarez, G.; Baró, M. D.; Miron, M.; Rodmacq, B.; Dieny, B.; Nogués, J.

    2008-04-01

    Exchange bias effects have been studied in elliptical dots composed of ferromagnetic Ni80Fe20-antiferromagnetic Ir20Mn80 bilayers. The magnetization reversal mechanisms and magnetic configurations have been investigated by magneto-optic Kerr effect and magnetic force microscopy. Although the obtained bias fields in these dots are relatively small, the magnetization reversal is found to be influenced by the ferromagnetic-antiferromagnetic coupling. Namely, for some off-axis angles of measurement, the magnetization reversal mechanism of the Ni80Fe20-Ir20Mn80 ellipses depends on whether exchange bias is induced along the minor or major axis of the ellipses. Hence, exchange bias is shown to be an effective means for tailoring the magnetization reversal of elliptical dots after sample fabrication.

  9. Selection bias in dynamically measured supermassive black hole samples: scaling relations and correlations between residuals in semi-analytic galaxy formation models

    NASA Astrophysics Data System (ADS)

    Barausse, Enrico; Shankar, Francesco; Bernardi, Mariangela; Dubois, Yohan; Sheth, Ravi K.

    2017-07-01

    Recent work has confirmed that the scaling relations between the masses of supermassive black holes and host-galaxy properties such as stellar masses and velocity dispersions may be biased high. Much of this may be caused by the requirement that the black hole sphere of influence must be resolved for the black hole mass to be reliably estimated. We revisit this issue with a comprehensive galaxy evolution semi-analytic model. Once tuned to reproduce the (mean) correlation of black hole mass with velocity dispersion, the model cannot account for the correlation with stellar mass. This is independent of the model's parameters, thus suggesting an internal inconsistency in the data. The predicted distributions, especially at the low-mass end, are also much broader than observed. However, if selection effects are included, the model's predictions tend to align with the observations. We also demonstrate that the correlations between the residuals of the scaling relations are more effective than the relations themselves at constraining models for the feedback of active galactic nuclei (AGNs). In fact, we find that our model, while in apparent broad agreement with the scaling relations when accounting for selection biases, yields very weak correlations between their residuals at fixed stellar mass, in stark contrast with observations. This problem persists when changing the AGN feedback strength, and is also present in the hydrodynamic cosmological simulation Horizon-AGN, which includes state-of-the-art treatments of AGN feedback. This suggests that current AGN feedback models are too weak or simply not capturing the effect of the black hole on the stellar velocity dispersion.

  10. Characterizing dye bias in microarray experiments.

    PubMed

    Dobbin, K K; Kawasaki, E S; Petersen, D W; Simon, R M

    2005-05-15

    Spot intensity serves as a proxy for gene expression in dual-label microarray experiments. Dye bias is defined as an intensity difference between samples labeled with different dyes attributable to the dyes instead of the gene expression in the samples. Dye bias that is not removed by array normalization can introduce bias into comparisons between samples of interest. But if the bias is consistent across samples for the same gene, it can be corrected by proper experimental design and analysis. If the dye bias is not consistent across samples for the same gene, but is different for different samples, then removing the bias becomes more problematic, perhaps indicating a technical limitation to the ability of fluorescent signals to accurately represent gene expression. Thus, it is important to characterize dye bias to determine: (1) whether it will be removed for all genes by array normalization, (2) whether it will not be removed by normalization but can be removed by proper experimental design and analysis and (3) whether dye bias correction is more problematic than either of these and is not easily removable. We analyzed two large (each >27 arrays) tissue culture experiments with extensive dye swap arrays to better characterize dye bias. Indirect, amino-allyl labeling was used in both experiments. We found that post-normalization dye bias that is consistent across samples does appear to exist for many genes, and that controlling and correcting for this type of dye bias in design and analysis is advisable. The extent of this type of dye bias remained unchanged under a wide range of normalization methods (median-centering, various loess normalizations) and statistical analysis techniques (parametric, rank based, permutation based, etc.). We also found dye bias related to the individual samples for a much smaller subset of genes. But these sample-specific dye biases appeared to have minimal impact on estimated gene-expression differences between the cell lines.

  11. Statistical biases in stellar astronomy: the Malmquist bias revisited

    NASA Astrophysics Data System (ADS)

    Butkevich, A. G.; Berdyugin, A. V.; Teerikorpi, P.

    2005-09-01

    A unified analytical treatment of the Malmquist bias is presented. Depending on the data under consideration and on the way the mean values of absolute magnitude are calculated, three different types of Malmquist bias appear: integral bias, and magnitude- and distance-dependent ones. An analytical consideration of the distance-dependent bias, previously studied in extragalactic astronomy, is given in terms of the trigonometric parallax. In a quantitative treatment of the Spaenhauer diagram, in which the derived absolute magnitude is plotted versus the true parallax, we developed an easy-to-use method for determination of the region unaffected by the bias (`unbiased plateau'). Considering spectroscopic distance indicators, we point out that for any magnitude-limited sample spectroscopic distance and parallax approach constant limits as the true distance increases. We draw some examples from luminosity calibrations of stellar classes. A brief outline is also given of a tentative course of investigations, anticipating future space astrometry missions.

  12. Types of Research Bias Encountered in IR.

    PubMed

    Gabr, Ahmed; Kallini, Joseph Ralph; Desai, Kush; Hickey, Ryan; Thornburg, Bartley; Kulik, Laura; Lewandowski, Robert J; Salem, Riad

    2016-04-01

    Bias is a systemic error in studies that leads to inaccurate deductions. Relevant biases in the field of IR and interventional oncology were identified after reviewing articles published in the Journal of Vascular and Interventional Radiology and CardioVascular and Interventional Radiology. Biases cited in these articles were divided into three categories: preinterventional (health care access, participation, referral, and sample biases), periinterventional (contamination, investigator, and operator biases), and postinterventional (guarantee-time, lead time, loss to follow-up, recall, and reporting biases). Copyright © 2016 SIR. Published by Elsevier Inc. All rights reserved.

  13. Exchange-biased magnetic vortices.

    SciTech Connect

    Hoffmann, A.; Sort, J.; Buchanan, K. S.; Nogues, J.; Inst. Catalana de Recerca i Estudis Avancats; Univ. Autonoma de Barcelona

    2008-07-01

    This paper reviews our work on the interplay between exchange bias due to the coupling of a ferromagnet to an antiferromagnet and the formation of magnetic vortices, which occur due to the patterning of a ferromagnet. Depending on the thermal and magnetic history, a variety of different effects can be observed. Thermal annealing in a saturating magnetic field establishes a spatially homogeneous exchange bias with a uniform unidirectional anisotropy. This results in an angular dependence of the magnetization reversal mode, which can be either via magnetization rotation or vortex nucleation and annihilation. In contrast, thermal annealing in a field smaller than the vortex annihilation field imprints the ferromagnetic vortex configuration in the antiferromagnet with high fidelity resulting in unusual asymmetric hysteresis loops. Furthermore, we discuss how the interfacial nature of the exchange bias can modify the vortex magnetization along the thickness of the ferromagnet.

  14. Understanding Errors, Biases that Can Affect Journalists.

    ERIC Educational Resources Information Center

    Stocking, S. Holly; Gross, Paget H.

    1989-01-01

    Outlines some of the errors and biases in thinking that psychologists have documented in recent years, including the eyewitness fallacy, underutilization of statistics, confirmation bias, misperceptions of risk, sample errors and biases, and misunderstanding of regression. Argues that journalism educators need to bring these to the attention of…

  15. Sequential biases in accumulating evidence

    PubMed Central

    Huggins, Richard; Dogo, Samson Henry

    2015-01-01

    Whilst it is common in clinical trials to use the results of tests at one phase to decide whether to continue to the next phase and to subsequently design the next phase, we show that this can lead to biased results in evidence synthesis. Two new kinds of bias associated with accumulating evidence, termed ‘sequential decision bias’ and ‘sequential design bias’, are identified. Both kinds of bias are the result of making decisions on the usefulness of a new study, or its design, based on the previous studies. Sequential decision bias is determined by the correlation between the value of the current estimated effect and the probability of conducting an additional study. Sequential design bias arises from using the estimated value instead of the clinically relevant value of an effect in sample size calculations. We considered both the fixed‐effect and the random‐effects models of meta‐analysis and demonstrated analytically and by simulations that in both settings the problems due to sequential biases are apparent. According to our simulations, the sequential biases increase with increased heterogeneity. Minimisation of sequential biases arises as a new and important research area necessary for successful evidence‐based approaches to the development of science. © 2015 The Authors. Research Synthesis Methods Published by John Wiley & Sons Ltd. PMID:26626562

  16. Berkson's bias, selection bias, and missing data.

    PubMed

    Westreich, Daniel

    2012-01-01

    Although Berkson's bias is widely recognized in the epidemiologic literature, it remains underappreciated as a model of both selection bias and bias due to missing data. Simple causal diagrams and 2 × 2 tables illustrate how Berkson's bias connects to collider bias and selection bias more generally, and show the strong analogies between Berksonian selection bias and bias due to missing data. In some situations, considerations of whether data are missing at random or missing not at random are less important than the causal structure of the missing data process. Although dealing with missing data always relies on strong assumptions about unobserved variables, the intuitions built with simple examples can provide a better understanding of approaches to missing data in real-world situations.

  17. A Study of Program Management Procedures in the Campus-Based and Basic Grant Programs. Technical Report No. 1: Sample Design, Student Survey Yield and Bias.

    ERIC Educational Resources Information Center

    Puma, Michael J.; Ellis, Richard

    Part of a study of program management procedures in the campus-based and Basic Educational Opportunity Grant programs reports on the design of the site visit component of the study and the results of the student survey, both in terms of the yield obtained and the quality of the data. Chapter 2 describes the design of sampling methodology employed…

  18. Some Computational Details of Configural Sampling Methods.

    DTIC Science & Technology

    1981-03-30

    HSfigKEjBl :rfr| ř=bi: -rffvff-lTE IS 1Ä t*j^ "iitf TH : Wttttg: a St fly Sä T: n >« » cu* u« ÖSS tU » asmi *mm *~> 5344 •St -JTT +tÖ -H+L Uli k... PFE ^F Pa (C(rr’I)+C(vv?) )/?.Fn cse’~ (*ü?2) -C (PF ] ) •ypÄvqprp i ri"s Tp C^,VF•’CTJP^’TT’>!’, rr 25^ r • i *? CC)>(C(I)-P)/f r*?T*F...FE’I*0 Z (3 *"") Trr’PS(57c) ,TE"P°(57r) , mE ,’P(c7P) CC""G!\\/-5FF* 1/2 , K/*F58 ’ /PC"*1/ orT/pPFa2/T , K, J/*PE"^/V/I PPB ? /"r?,r TVpsTVPAl

  19. Hindsight bias around the world.

    PubMed

    Pohl, Rüdiger F; Bender, Michael; Lachmann, Gregor

    2002-01-01

    Hindsight bias refers to the tendency to overestimate in hindsight what one has known in foresight. Recently, two experiments extended the research to include samples from different cultures (Choi & Nisbett, 2000; Heine & Lehman, 1996). Asking their participants what they would have guessed before they knew the outcome ("hypothetical design"), Choi and Nisbett (2000) found that Koreans, in comparison to North Americans, exhibited more hindsight bias. Heine and Lehman (1996), however, reported that Japanese people in comparison to Canadians showed marginally less hindsight bias. In a second study, in which participants were asked to recall what they had estimated before they knew the outcome ("memory design"), the latter authors found no difference in hindsight bias between Japanese people and Canadians. We extended these studies with 225 Internet participants, in a hypothetical design, from four different continents (Asia, Australia, Europe, and North America). Hindsight bias was large and similar for all samples except for German and Dutch participants who showed no hindsight bias at all. While the latter effect may be based on peculiarities of the material and of the participants, the former underscores the worldwide stability of the phenomenon. In addition a follow-up surprise rating (paper and pencil) in China (35 participants) and Germany (20 participants) revealed that only less surprising items led to hindsight bias while more surprising ones did not. We suggest that the basic cognitive processes leading to hindsight bias are by-products of the evolutionary-evolved capacity of adaptive learning. On top of these basic processes, individual meta-cognitions (e.g., elicited by surprise) or motives (e.g., a self-serving motive) may further moderate the amount of bias, thus explaining the diverging results of Choi and Nisbett (2000), Heine and Lehman (1996), and our own study.

  20. Configuration Management Policy

    EPA Pesticide Factsheets

    This Policy establishes an Agency-wide Configuration Management Program and to provide responsibilities, compliance requirements, and overall principles for Configuration and Change Management processes to support information technology management.

  1. Operational Dynamic Configuration Analysis

    NASA Technical Reports Server (NTRS)

    Lai, Chok Fung; Zelinski, Shannon

    2010-01-01

    Sectors may combine or split within areas of specialization in response to changing traffic patterns. This method of managing capacity and controller workload could be made more flexible by dynamically modifying sector boundaries. Much work has been done on methods for dynamically creating new sector boundaries [1-5]. Many assessments of dynamic configuration methods assume the current day baseline configuration remains fixed [6-7]. A challenging question is how to select a dynamic configuration baseline to assess potential benefits of proposed dynamic configuration concepts. Bloem used operational sector reconfigurations as a baseline [8]. The main difficulty is that operational reconfiguration data is noisy. Reconfigurations often occur frequently to accommodate staff training or breaks, or to complete a more complicated reconfiguration through a rapid sequence of simpler reconfigurations. Gupta quantified a few aspects of airspace boundary changes from this data [9]. Most of these metrics are unique to sector combining operations and not applicable to more flexible dynamic configuration concepts. To better understand what sort of reconfigurations are acceptable or beneficial, more configuration change metrics should be developed and their distribution in current practice should be computed. This paper proposes a method to select a simple sequence of configurations among operational configurations to serve as a dynamic configuration baseline for future dynamic configuration concept assessments. New configuration change metrics are applied to the operational data to establish current day thresholds for these metrics. These thresholds are then corroborated, refined, or dismissed based on airspace practitioner feedback. The dynamic configuration baseline selection method uses a k-means clustering algorithm to select the sequence of configurations and trigger times from a given day of operational sector combination data. The clustering algorithm selects a simplified

  2. Configuration Analysis Tool

    NASA Technical Reports Server (NTRS)

    Merwarth, P. D.

    1983-01-01

    Configuration Analysis Tool (CAT), is information storage and report generation system for aid of configuration management activities. Configuration management is discipline composed of many techniques selected to track and direct evolution of complex systems. CAT is interactive program that accepts, organizes and stores information pertinent to specific phases of project.

  3. Context Matters: Volunteer Bias, Small Sample Size, and the Value of Comparison Groups in the Assessment of Research-Based Undergraduate Introductory Biology Lab Courses

    PubMed Central

    Brownell, Sara E.; Kloser, Matthew J.; Fukami, Tadashi; Shavelson, Richard J.

    2013-01-01

    The shift from cookbook to authentic research-based lab courses in undergraduate biology necessitates the need for evaluation and assessment of these novel courses. Although the biology education community has made progress in this area, it is important that we interpret the effectiveness of these courses with caution and remain mindful of inherent limitations to our study designs that may impact internal and external validity. The specific context of a research study can have a dramatic impact on the conclusions. We present a case study of our own three-year investigation of the impact of a research-based introductory lab course, highlighting how volunteer students, a lack of a comparison group, and small sample sizes can be limitations of a study design that can affect the interpretation of the effectiveness of a course. PMID:24358380

  4. Quantifying the degree of bias from using county-scale data in species distribution modeling: Can increasing sample size or using county-averaged environmental data reduce distributional overprediction?

    PubMed

    Collins, Steven D; Abbott, John C; McIntyre, Nancy E

    2017-08-01

    Citizen-science databases have been used to develop species distribution models (SDMs), although many taxa may be only georeferenced to county. It is tacitly assumed that SDMs built from county-scale data should be less precise than those built with more accurate localities, but the extent of the bias is currently unknown. Our aims in this study were to illustrate the effects of using county-scale data on the spatial extent and accuracy of SDMs relative to true locality data and to compare potential compensatory methods (including increased sample size and using overall county environmental averages rather than point locality environmental data). To do so, we developed SDMs in maxent with PRISM-derived BIOCLIM parameters for 283 and 230 species of odonates (dragonflies and damselflies) and butterflies, respectively, for five subsets from the OdonataCentral and Butterflies and Moths of North America citizen-science databases: (1) a true locality dataset, (2) a corresponding sister dataset of county-centroid coordinates, (3) a dataset where the average environmental conditions within each county were assigned to each record, (4) a 50/50% mix of true localities and county-centroid coordinates, and (5) a 50/50% mix of true localities and records assigned the average environmental conditions within each county. These mixtures allowed us to quantify the degree of bias from county-scale data. Models developed with county centroids overpredicted the extent of suitable habitat by 15% on average compared to true locality models, although larger sample sizes (>100 locality records) reduced this disparity. Assigning county-averaged environmental conditions did not offer consistent improvement, however. Because county-level data are of limited value for developing SDMs except for species that are widespread and well collected or that inhabit regions where small, climatically uniform counties predominate, three means of encouraging more accurate georeferencing in citizen

  5. Analytical Bias Exceeding Desirable Quality Goal in 4 out of 5 Common Immunoassays: Results of a Native Single Serum Sample External Quality Assessment Program for Cobalamin, Folate, Ferritin, Thyroid-Stimulating Hormone, and Free T4 Analyses.

    PubMed

    Kristensen, Gunn B B; Rustad, Pål; Berg, Jens P; Aakre, Kristin M

    2016-09-01

    We undertook this study to evaluate method differences for 5 components analyzed by immunoassays, to explore whether the use of method-dependent reference intervals may compensate for method differences, and to investigate commutability of external quality assessment (EQA) materials. Twenty fresh native single serum samples, a fresh native serum pool, Nordic Federation of Clinical Chemistry Reference Serum X (serum X) (serum pool), and 2 EQA materials were sent to 38 laboratories for measurement of cobalamin, folate, ferritin, free T4, and thyroid-stimulating hormone (TSH) by 5 different measurement procedures [Roche Cobas (n = 15), Roche Modular (n = 4), Abbott Architect (n = 8), Beckman Coulter Unicel (n = 2), and Siemens ADVIA Centaur (n = 9)]. The target value for each component was calculated based on the mean of method means or measured by a reference measurement procedure (free T4). Quality specifications were based on biological variation. Local reference intervals were reported from all laboratories. Method differences that exceeded acceptable bias were found for all components except folate. Free T4 differences from the uncommonly used reference measurement procedure were large. Reference intervals differed between measurement procedures but also within 1 measurement procedure. The serum X material was commutable for all components and measurement procedures, whereas the EQA materials were noncommutable in 13 of 50 occasions (5 components, 5 methods, 2 EQA materials). The bias between the measurement procedures was unacceptably large in 4/5 tested components. Traceability to reference materials as claimed by the manufacturers did not lead to acceptable harmonization. Adjustment of reference intervals in accordance with method differences and use of commutable EQA samples are not implemented commonly. © 2016 American Association for Clinical Chemistry.

  6. Use of Ga for mass bias correction for the accurate determination of copper isotope ratio in the NIST SRM 3114 Cu standard and geological samples by MC-ICP MS

    NASA Astrophysics Data System (ADS)

    Zhang, T.; Zhou, L.; Tong, S.

    2015-12-01

    The absolute determination of the Cu isotope ratio in NIST SRM 3114 based on a regression mass bias correction model is performed for the first time with NIST SRM 944 Ga as the calibrant. A value of 0.4471±0.0013 (2SD, n=37) for the 65Cu/63Cu ratio was obtained with a value of +0.18±0.04 ‰ (2SD, n=5) for δ65Cu relative to NIST 976.The availability of the NIST SRM 3114 material, now with the absolute value of the 65Cu/63Cu ratio and a δ65Cu value relative to NIST 976 makes it suitable as a new candidate reference material for Cu isotope studies. In addition, a protocol is described for the accurate and precise determination of δ65Cu values of geological reference materials. Purification of Cu from the sample matrix was performed using the AG MP-1M Bio-Rad resin. The column recovery for geological samples was found to be 100±2% (2SD, n=15).A modified method of standard-sample bracketing with internal normalization for mass bias correction was employed by adding natural Ga to both the sample and the solution of NIST SRM 3114, which was used as the bracketing standard. An absolute value of 0.4471±0.0013 (2SD, n=37) for 65Cu/63Cu quantified in this study was used to calibrate the 69Ga/71Ga ratio in the two adjacent bracketing standards of SRM 3114,their average value of 69Ga/71Ga was then used to correct the 65Cu/63Cu ratio in the sample. Measured δ65Cu values of 0.18±0.04‰ (2SD, n=20),0.13±0.04‰ (2SD, n=9),0.08±0.03‰ (2SD, n=6),0.01±0.06‰(2SD, n=4) and 0.26±0.04‰ (2SD, n=7) were obtained for five geological reference materials of BCR-2,BHVO-2,AGV-2,BIR-1a,and GSP-2,respectively,in agreement with values obtained in previous studies.

  7. Electrically biased GaAs/AlGaAs heterostructures for enhanced detection of bacteria

    NASA Astrophysics Data System (ADS)

    Aziziyan, Mohammad R.; Hassen, Walid M.; Dubowski, Jan J.

    2016-03-01

    We have examined the influence of electrical bias on immobilization of bacteria on the surface of GaAs/AlGaAs heterostructures, functionalized with an alkanethiol based architecture. A mixture of biotinylated polyethylene glycol (PEG) thiol and hexadecanethiol was applied to attach neutravidin and antibodies targeting specific immobilization of Legionella pneumophila. An electrochemical setup was designed to bias biofunctionalized samples with the potential measured versus silver/silver chloride reference electrode in a three electrode configuration system. The immobilization efficiency has been examined with fluorescence microscopy after tagging captured bacteria with fluorescein labeled antibodies. We demonstrate more than 2 times enhanced capture of Legionella pneumophila, suggesting the potential of electrically biased biochips to deliver enhanced sensitivity in detecting these bacteria.

  8. Configurable hot spot fixing system

    NASA Astrophysics Data System (ADS)

    Kajiwara, Masanari; Kobayashi, Sachiko; Mashita, Hiromitsu; Aburada, Ryota; Furuta, Nozomu; Kotani, Toshiya

    2014-03-01

    Hot spot fixing (HSF) method has been used to fix many hot spots automatically. However, conventional HSF based on a biasing based modification is difficult to fix many hot spots under a low-k1 lithography condition. In this paper we proposed a new HSF, called configurable hotspot fixing system. The HSF has two major concepts. One is a new function to utilize vacant space around a hot spot by adding new patterns or extending line end edges around the hot spot. The other is to evaluate many candidates at a time generated by the new functions. We confirmed the proposed HSF improves 73% on the number of fixing hot spots and reduces total fixing time by 50% on a device layout equivalent to 28nm-node. The result shows the proposed HSF is effective for layouts under the low-k1 lithography condition.

  9. Computer Lab Configuration.

    ERIC Educational Resources Information Center

    Wodarz, Nan

    2003-01-01

    Describes the layout and elements of an effective school computer lab. Includes configuration, storage spaces, cabling and electrical requirements, lighting, furniture, and computer hardware and peripherals. (PKP)

  10. Computer Lab Configuration.

    ERIC Educational Resources Information Center

    Wodarz, Nan

    2003-01-01

    Describes the layout and elements of an effective school computer lab. Includes configuration, storage spaces, cabling and electrical requirements, lighting, furniture, and computer hardware and peripherals. (PKP)

  11. Perceptual Biases in Processing Facial Identity and Emotion

    ERIC Educational Resources Information Center

    Coolican, Jamesie; Eskes, Gail A.; McMullen, Patricia A.; Lecky, Erin

    2008-01-01

    Normal observers demonstrate a bias to process the left sides of faces during perceptual judgments about identity or emotion. This effect suggests a right cerebral hemisphere processing bias. To test the role of the right hemisphere and the involvement of configural processing underlying this effect, young and older control observers and patients…

  12. Do the Kaufman tests of cognitive ability and academic achievement display construct bias across a representative sample of Black, Hispanic, and Caucasian school-age children in grades 1 through 12?

    PubMed

    Scheiber, Caroline

    2016-08-01

    As the demographic profile in the United States continues to change and becomes ethnically more diverse, the need for culturally appropriate test instruments has become a national concern among educators, clinicians, and researchers. The Kaufman Assessment Battery for Children-2nd Edition (KABC-II) and the Kaufman Test of Educational Achievement-2nd Edition (KTEA-II) are 2 popular tests of intelligence and achievement, known to appeal to an ethnically diverse client population. The present study investigated test bias in terms of the test scores' construct validity across a nationally representative sample of Caucasian, Black, and Hispanic (N = 2,001) children in Grades 1-12. Confirmatory factor analysis was used to assess whether increasing sets of equality constraints fit the test scores' underlying theoretical model equally well for all 3 ethnic groups. Results showed that factorial invariance of the factor structure, based on 7 Cattell-Horn-Carroll (CHC) model broad abilities, was met for all 3 groups. Outcomes contribute to a scarce body of literature on ethnic test bias that goes beyond the simple comparison of mean score differences. Results of this study provide the evidence needed to justify continuous use of the KABC-II and KTEA-II in the assessment of minority group children and adolescents. Furthermore, findings are generalizable beyond the Kaufman tests to other popular tests of intelligence and achievement; this is because this study is based on the CHC factor structure, a universal theory of cognition that is used as the theoretical underpinning by many well-known tests of intelligence and achievement, including the most recent versions of the Wechsler scales. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  13. An Overview of Particle Sampling Bias

    NASA Technical Reports Server (NTRS)

    Meyers, James F.; Edwards, Robert V.

    1984-01-01

    The complex relation between particle arrival statistics and the interarrival statistics is explored. It is known that the mean interarrival time given an initial velocity is generally not the inverse of the mean rate corresponding to that velocity. Necessary conditions for the measurement of the conditional rate are given.

  14. PIV Logon Configuration Guidance

    SciTech Connect

    Lee, Glen Alan

    2016-03-04

    This document details the configurations and enhancements implemented to support the usage of federal Personal Identity Verification (PIV) Card for logon on unclassified networks. The guidance is a reference implementation of the configurations and enhancements deployed at the Los Alamos National Laboratory (LANL) by Network and Infrastructure Engineering – Core Services (NIE-CS).

  15. FIP bias in a sigmoidal active region

    NASA Astrophysics Data System (ADS)

    Baker, D.; Brooks, D. H.; Démoulin, P.; van Driel-Gesztelyi, Lidia; Green, L. M.; Steed, K.; Carlyle, J.

    2014-01-01

    We investigate first ionization potential (FIP) bias levels in an anemone active region (AR) - coronal hole (CH) complex using an abundance map derived from Hinode/EIS spectra. The detailed, spatially resolved abundance map has a large field of view covering 359'' × 485''. Plasma with high FIP bias, or coronal abundances, is concentrated at the footpoints of the AR loops whereas the surrounding CH has a low FIP bias, ~1, i.e. photospheric abundances. A channel of low FIP bias is located along the AR's main polarity inversion line containing a filament where ongoing flux cancellation is observed, indicating a bald patch magnetic topology characteristic of a sigmoid/flux rope configuration.

  16. Recalibrating Academic Bias

    ERIC Educational Resources Information Center

    Yancey, George

    2012-01-01

    Whether political and/or religious academic bias exists is a question with important ramifications for the educational institutions. Those arguing for the presence of such bias contend that political conservatives and the highly religious in academia are marginalized and face discrimination. The question of academic bias tends to be cast in a…

  17. Oaths and hypothetical bias.

    PubMed

    Stevens, T H; Tabatabaei, Maryam; Lass, Daniel

    2013-09-30

    Results from experiments using an oath to eliminate hypothetical bias in stated preference valuation are presented. An oath has several potential advantages relative to other methods for reducing hypothetical bias. Our empirical results suggest that with an oath, mean hypothetical payments are not different from mean actual payments and that when controlling for experimental participants' characteristics using regression analyses, the oath eliminated hypothetical bias.

  18. Demonstrating the Correspondence Bias

    ERIC Educational Resources Information Center

    Howell, Jennifer L.; Shepperd, James A.

    2011-01-01

    Among the best-known and most robust biases in person perception is the correspondence bias--the tendency for people to make dispositional, rather than situational, attributions for an actor's behavior. The correspondence bias appears in virtually every social psychology textbook and in many introductory psychology textbooks, yet the authors'…

  19. Demonstrating the Correspondence Bias

    ERIC Educational Resources Information Center

    Howell, Jennifer L.; Shepperd, James A.

    2011-01-01

    Among the best-known and most robust biases in person perception is the correspondence bias--the tendency for people to make dispositional, rather than situational, attributions for an actor's behavior. The correspondence bias appears in virtually every social psychology textbook and in many introductory psychology textbooks, yet the authors'…

  20. Exploratory Studies of Bias in Achievement Tests.

    ERIC Educational Resources Information Center

    Green, Donald Ross; Draper, John F.

    This paper considers the question of bias in group administered academic achievement tests, bias which is inherent in the instruments themselves. A body of data on the test of performance of three disadvantaged minority groups--northern, urban black; southern, rural black; and, southwestern, Mexican-Americans--as tryout samples in contrast to…

  1. Method and apparatus configured for identification of a material

    DOEpatents

    Slater, John M.; Crawford, Thomas M.

    2000-01-01

    The present invention includes an apparatus configured for identification of a material, and methods of identifying a material. One embodiment of the invention provides an apparatus including a first region configured to receive a first sample, the first region being configured to output a first spectrum corresponding to the first sample and responsive to exposure of the first sample to radiation; a modulator configured to modulate the first spectrum according to a first frequency; a second region configured to receive a second sample, the second region being configured to output a second spectrum corresponding to the second sample and responsive to exposure of the second sample to the modulated first spectrum; and a detector configured to detect the second spectrum having a second frequency greater than the first frequency.

  2. Diamond nucleation under bias conditions

    SciTech Connect

    Stoeckel, R.; Stammler, M.; Janischowsky, K.; Ley, L.; Albrecht, M.; Strunk, H.P.

    1998-01-01

    The so-called bias pretreatment allows the growth of heteroepitaxial diamond films by plasma chemical vapor deposition on silicon (100) surfaces. We present plan-view and cross-sectional transmission electron micrographs of the substrate surface at different phases of the bias pretreatment. These observations are augmented by measurements of the etch rates of Si, SiC, and different carbon modifications under plasma conditions and the size distribution of oriented diamond crystals grown after bias pretreatment. Based on these results a new model for diamond nucleation under bias conditions is proposed. First, a closed layer of nearly epitaxially oriented cubic SiC with a thickness of about 10 nm is formed. Subplantation of carbon into this SiC layer causes a supersaturation with carbon and results in the subcutaneous formation of epitaxially oriented nucleation centers in the SiC layer. Etching of the SiC during the bias pretreatment as well as during diamond growth brings these nucleation centers to the sample surface and causes the growth of diamonds epitaxially oriented on the Si/SiC substrate. {copyright} {ital 1998 American Institute of Physics.}

  3. Halo assembly bias from Separate Universe simulations

    NASA Astrophysics Data System (ADS)

    Paranjape, Aseem; Padmanabhan, Nikhil

    2017-07-01

    We present a calibration of halo assembly bias using the Separate Universe technique. Specifically, we measure the response of halo abundances at fixed mass and concentration to the presence of an infinite-wavelength initial perturbation. We develop an analytical framework for describing the concentration dependence of this peak-background split halo bias - a measure of assembly bias - relying on the near-lognormal distribution of halo concentration at fixed halo mass. The combination of this analytical framework and the Separate Universe technique allows us to achieve very high precision in the calibration of the linear assembly bias b1, and qualitatively reproduces known trends such as the monotonic decrease (increase) of b1 with halo concentration at large (small) masses. The same framework extends to the concentration dependence of higher order bias parameters bn, and we present the first calibration of assembly bias in b2. Our calibrations are directly applicable in analytical Halo Model calculations that seek to robustly detect galaxy assembly bias in observational samples. We detect a non-universality in the b1-b2 relation arising from assembly bias, and suggest that simultaneous measurements of these bias parameters could be used to both detect the signature of assembly bias as well as mitigate its effects in cosmological analyses.

  4. Queries for Bias Testing

    NASA Technical Reports Server (NTRS)

    Gordon, Diana F.

    1992-01-01

    Selecting a good bias prior to concept learning can be difficult. Therefore, dynamic bias adjustment is becoming increasingly popular. Current dynamic bias adjustment systems, however, are limited in their ability to identify erroneous assumptions about the relationship between the bias and the target concept. Without proper diagnosis, it is difficult to identify and then remedy faulty assumptions. We have developed an approach that makes these assumptions explicit, actively tests them with queries to an oracle, and adjusts the bias based on the test results.

  5. Is probabilistic bias analysis approximately Bayesian?

    PubMed Central

    MacLehose, Richard F.; Gustafson, Paul

    2011-01-01

    Case-control studies are particularly susceptible to differential exposure misclassification when exposure status is determined following incident case status. Probabilistic bias analysis methods have been developed as ways to adjust standard effect estimates based on the sensitivity and specificity of exposure misclassification. The iterative sampling method advocated in probabilistic bias analysis bears a distinct resemblance to a Bayesian adjustment; however, it is not identical. Furthermore, without a formal theoretical framework (Bayesian or frequentist), the results of a probabilistic bias analysis remain somewhat difficult to interpret. We describe, both theoretically and empirically, the extent to which probabilistic bias analysis can be viewed as approximately Bayesian. While the differences between probabilistic bias analysis and Bayesian approaches to misclassification can be substantial, these situations often involve unrealistic prior specifications and are relatively easy to detect. Outside of these special cases, probabilistic bias analysis and Bayesian approaches to exposure misclassification in case-control studies appear to perform equally well. PMID:22157311

  6. Renormalized halo bias

    SciTech Connect

    Assassi, Valentin; Baumann, Daniel; Green, Daniel; Zaldarriaga, Matias E-mail: dbaumann@damtp.cam.ac.uk E-mail: matiasz@ias.edu

    2014-08-01

    This paper provides a systematic study of renormalization in models of halo biasing. Building on work of McDonald, we show that Eulerian biasing is only consistent with renormalization if non-local terms and higher-derivative contributions are included in the biasing model. We explicitly determine the complete list of required bias parameters for Gaussian initial conditions, up to quartic order in the dark matter density contrast and at leading order in derivatives. At quadratic order, this means including the gravitational tidal tensor, while at cubic order the velocity potential appears as an independent degree of freedom. Our study naturally leads to an effective theory of biasing in which the halo density is written as a double expansion in fluctuations and spatial derivatives. We show that the bias expansion can be organized in terms of Galileon operators which aren't renormalized at leading order in derivatives. Finally, we discuss how the renormalized bias parameters impact the statistics of halos.

  7. "Catching" Social Bias.

    PubMed

    Skinner, Allison L; Meltzoff, Andrew N; Olson, Kristina R

    2017-02-01

    Identifying the origins of social bias is critical to devising strategies to overcome prejudice. In two experiments, we tested the hypothesis that young children can catch novel social biases from brief exposure to biased nonverbal signals demonstrated by adults. Our results are consistent with this hypothesis. In Experiment 1, we found that children who were exposed to a brief video depicting nonverbal bias in favor of one individual over another subsequently explicitly preferred, and were more prone to behave prosocially toward, the target of positive nonverbal signals. Moreover, in Experiment 2, preschoolers generalized such bias to other individuals. The spread of bias observed in these experiments lays a critical foundation for understanding the way that social biases may develop and spread early in childhood.

  8. Compact Torsatron configurations

    SciTech Connect

    Carreras, B. A.; Dominguez, N.; Garcia, L.; Lynch, V. E.; Lyon, J. F.; Cary, J. R.; Hanson, J. D.; Navarro, A. P.

    1987-09-01

    Low-aspect-ratio stellarator configurations can be realized by using torsatron winding. Plasmas with aspect ratios in the range of 3.5 to 5 can be confined by these Compact Torsatron configurations. Stable operation at high BETA should be possible in these devices, if a vertical field coil system is adequately designed to avoid breaking of the magnetic surfaces at finite BETA. 17 refs., 21 figs., 1 tab.

  9. The TPX configuration

    SciTech Connect

    Brown, T.G.

    1994-11-01

    The TPX configuration has progressed since the March, 1993 Conceptual Design Review (CDR). Changes have been made to enhance operating performance and improve engineering design margins. Clearances have been added to subsystem envelopes to increase fabrication space and expand assembly tolerances; design modifications have been adopted to meet changes in physics requirements and to enhance maintenance features. Configuration details of magnet leads and services have been added and major subsystem clearance requirements for assembly/disassembly have been revisited.

  10. ION Configuration Editor

    NASA Technical Reports Server (NTRS)

    Borgen, Richard L.

    2013-01-01

    The configuration of ION (Inter - planetary Overlay Network) network nodes is a manual task that is complex, time-consuming, and error-prone. This program seeks to accelerate this job and produce reliable configurations. The ION Configuration Editor is a model-based smart editor based on Eclipse Modeling Framework technology. An ION network designer uses this Eclipse-based GUI to construct a data model of the complete target network and then generate configurations. The data model is captured in an XML file. Intrinsic editor features aid in achieving model correctness, such as field fill-in, type-checking, lists of valid values, and suitable default values. Additionally, an explicit "validation" feature executes custom rules to catch more subtle model errors. A "survey" feature provides a set of reports providing an overview of the entire network, enabling a quick assessment of the model s completeness and correctness. The "configuration" feature produces the main final result, a complete set of ION configuration files (eight distinct file types) for each ION node in the network.

  11. Implicit Social Biases in People With Autism.

    PubMed

    Birmingham, Elina; Stanley, Damian; Nair, Remya; Adolphs, Ralph

    2015-11-01

    Implicit social biases are ubiquitous and are known to influence social behavior. A core diagnostic criterion of autism spectrum disorders (ASD) is abnormal social behavior. We investigated the extent to which individuals with ASD might show a specific attenuation of implicit social biases, using Implicit Association Tests (IATs) involving social (gender, race) and nonsocial (nature, shoes) categories. High-functioning adults with ASD showed intact but reduced IAT effects relative to healthy control participants. We observed no selective attenuation of implicit social (vs. nonsocial) biases in our ASD population. To extend these results, we supplemented our healthy control data with data collected from a large online sample from the general population and explored correlations between autistic traits and IAT effects. We observed no systematic relationship between autistic traits and implicit social biases in our online and control samples. Taken together, these results suggest that implicit social biases, as measured by the IAT, are largely intact in ASD. © The Author(s) 2015.

  12. From exchange bias to magnetic memory

    NASA Astrophysics Data System (ADS)

    Chesnel, Karine; Kevan, Steve; Fullerton, Eric; Kortright, Jeff; Hellwig, Olav; Wilcken, Brian; Nelson, Joe

    2008-10-01

    Magnetic memory, the ability of a material to remember its magnetic domains spatial configuration throughout magnetization cycling, is a key feature in ferromagnetic materials and offers potential technological interest for the data storage industry. One way to quantify the magnetic memory is to use Coherent X-ray Resonant Magnetic Scattering (XRMS) tools, at synchrotron facilities. The light is tuned to the resonant edge of the magnetic element to optimize the magneto-optical contrast. When illuminated by the coherent beam the sample produces speckle patterns that are collected on two dimensional detectors. Our approach is to cross-correlate patterns recorded at different field values throughout the magnetization cycle, and at different temperatures. We are particularly interested in the return point memory (RPM) and the conjugate point memory (CPM) that characterize the memory after a full, or half cycle respectively. We will give here an overview of different type of memory behaviors, first showing disorder induced memory in thin CoPt films and the influence of the film roughness, then demonstrating the ability to control the magnetic memory by inducing exchange bias. We will see how the local exchange couplings pin the magnetic domain in the ferromagnetic layer and lead the large memory enhancement.

  13. A separated bias identification and state estimation algorithm for nonlinear systems

    NASA Technical Reports Server (NTRS)

    Caglayan, A. K.; Lancraft, R. E.

    1983-01-01

    A computational algorithm for the identification of biases in discrete-time, nonlinear, stochastic systems is derived by extending the separate bias estimation results for linear systems to the extended Kalman filter formulation. The merits of the approach are illustrated by identifying instrument biases using a terminal configured vehicle simulation.

  14. Bias in research.

    PubMed

    Simundić, Ana-Maria

    2013-01-01

    By writing scientific articles we communicate science among colleagues and peers. By doing this, it is our responsibility to adhere to some basic principles like transparency and accuracy. Authors, journal editors and reviewers need to be concerned about the quality of the work submitted for publication and ensure that only studies which have been designed, conducted and reported in a transparent way, honestly and without any deviation from the truth get to be published. Any such trend or deviation from the truth in data collection, analysis, interpretation and publication is called bias. Bias in research can occur either intentionally or unintentionally. Bias causes false conclusions and is potentially misleading. Therefore, it is immoral and unethical to conduct biased research. Every scientist should thus be aware of all potential sources of bias and undertake all possible actions to reduce or minimize the deviation from the truth. This article describes some basic issues related to bias in research.

  15. Restructured Freedom configuration characteristics

    NASA Technical Reports Server (NTRS)

    Troutman, Patrick A.; Heck, Michael L.; Kumar, Renjith R.; Mazanek, Daniel D.

    1991-01-01

    In Jan. 1991, the LaRc SSFO performed an assessment of the configuration characteristics of the proposed pre-integrated Space Station Freedom (SSF) concept. Of particular concern was the relationship of solar array operation and orientation with respect to spacecraft controllability. For the man-tended configuration (MTC), it was determined that torque equilibrium attitude (TEA) seeking Control Moment Gyroscope (CMG) control laws could not always maintain attitude. The control problems occurred when the solar arrays were tracking the sun to produce full power while flying in an arrow or gravity gradient flight mode. The large solar array articulations that sometimes result from having the functions of the alpha and beta joints reversed on MTC induced large product of inertia changes that can invalidate the control system gains during an orbit. Several modified sun tracking techniques were evaluated with respect to producing a controllable configuration requiring no modifications to the CMG control algorithms. Another assessment involved the permanently manned configuration (PMC) which has a third asymmetric PV unit on one side of the transverse boom. Recommendations include constraining alpha rotations for MTC in the arrow and gravity gradient flight modes and perhaps developing new non-TEA seeking control laws. Recommendations for PMC include raising the operational altitude and moving to a symmetric configuration as soon as possible.

  16. Spatial Configurations: Erickson Reexamined.

    ERIC Educational Resources Information Center

    Budd, Barbara E.; And Others

    1985-01-01

    Erickson's 1951 study of gender differences in preadolescents' play construction was replicated and expanded to correct for sex bias of materials. Erickson's finding of innate biological differences in the experience and perception of space was not confirmed. Instead, differences were attributed to the materials provided. (KH)

  17. Interpretation biases in paranoia.

    PubMed

    Savulich, George; Freeman, Daniel; Shergill, Sukhi; Yiend, Jenny

    2015-01-01

    Information in the environment is frequently ambiguous in meaning. Emotional ambiguity, such as the stare of a stranger, or the scream of a child, encompasses possible good or bad emotional consequences. Those with elevated vulnerability to affective disorders tend to interpret such material more negatively than those without, a phenomenon known as "negative interpretation bias." In this study we examined the relationship between vulnerability to psychosis, measured by trait paranoia, and interpretation bias. One set of material permitted broadly positive/negative (valenced) interpretations, while another allowed more or less paranoid interpretations, allowing us to also investigate the content specificity of interpretation biases associated with paranoia. Regression analyses (n=70) revealed that trait paranoia, trait anxiety, and cognitive inflexibility predicted paranoid interpretation bias, whereas trait anxiety and cognitive inflexibility predicted negative interpretation bias. In a group comparison those with high levels of trait paranoia were negatively biased in their interpretations of ambiguous information relative to those with low trait paranoia, and this effect was most pronounced for material directly related to paranoid concerns. Together these data suggest that a negative interpretation bias occurs in those with elevated vulnerability to paranoia, and that this bias may be strongest for material matching paranoid beliefs. We conclude that content-specific biases may be important in the cause and maintenance of paranoid symptoms.

  18. Software Configuration Management Guidebook

    NASA Technical Reports Server (NTRS)

    1995-01-01

    The growth in cost and importance of software to NASA has caused NASA to address the improvement of software development across the agency. One of the products of this program is a series of guidebooks that define a NASA concept of the assurance processes which are used in software development. The Software Assurance Guidebook, SMAP-GB-A201, issued in September, 1989, provides an overall picture of the concepts and practices of NASA in software assurance. Lower level guidebooks focus on specific activities that fall within the software assurance discipline, and provide more detailed information for the manager and/or practitioner. This is the Software Configuration Management Guidebook which describes software configuration management in a way that is compatible with practices in industry and at NASA Centers. Software configuration management is a key software development process, and is essential for doing software assurance.

  19. Gender Bias in SAT Items.

    ERIC Educational Resources Information Center

    Loewen, James W.; And Others

    Sex-related bias on the Scholastic Aptitude Test (SAT) was studied in a sample of 1,112 students in SAT coaching classes who took the SAT. Of these, 1,028 answered an additional questionnaire (Appendix A of this report) about high school grade point average, perceived abilities, and background. Almost all of the subjects were 11th graders (97.8%),…

  20. Using an Innovation Configuration Component Map To Assess the Relationship between Student Achievement and the Degree of Implementation of Extended School Services in a Sample of Kentucky Middle Schools.

    ERIC Educational Resources Information Center

    Craig, James R.; Kacer, Barbara A.

    One of the diagnostic tools used in the evaluation of programs implemented under the Kentucky Education Reform Act (KERA) (1990) is the Innovation Configuration Component (ICC) Map, designed to specify the key elements associated with an innovation and to define what "use" means in the context of implementing an innovation. This study…

  1. Electronically configured battery pack

    SciTech Connect

    Kemper, D.

    1997-03-01

    Battery packs for portable equipment must sometimes accommodate conflicting requirements to meet application needs. An electronically configurable battery pack was developed to support two highly different operating modes, one requiring very low power consumption at a low voltage and the other requiring high power consumption at a higher voltage. The configurable battery pack optimizes the lifetime and performance of the system by making the best use of all available energy thus enabling the system to meet its goals of operation, volume, and lifetime. This paper describes the cell chemistry chosen, the battery pack electronics, and tradeoffs made during the evolution of its design.

  2. Maternal Anxiety Predicts Attentional Bias Towards Threat in Infancy.

    PubMed

    Morales, Santiago; Brown, Kayla M; Taber-Thomas, Bradley C; LoBue, Vanessa; Buss, Kristin A; Pérez-Edgar, Koraly E

    2017-02-16

    Although cognitive theories of psychopathology suggest that attention bias toward threat plays a role in the etiology and maintenance of anxiety, there is relatively little evidence regarding individual differences in the earliest development of attention bias toward threat. The current study examines attention bias toward threat during its potential first emergence by evaluating the relations between attention bias and known risk factors of anxiety (i.e., temperamental negative affect and maternal anxiety). We measured attention bias to emotional faces in infants (N = 98; 57 male) ages 4 to 24 months during an attention disengagement eye-tracking paradigm. We hypothesized that (a) there would be an attentional bias toward threat in the full sample of infants, replicating previous studies; (b) attentional bias toward threat would be positively related to maternal anxiety; and (c) attention bias toward threat would be positively related to temperamental negative affect. Finally, (d) we explored the potential interaction between temperament and maternal anxiety in predicting attention bias toward threat. We found that attention bias to the affective faces did not change with age, and that bias was not related to temperament. However, attention bias to threat, but not attention bias to happy faces, was positively related to maternal anxiety, such that higher maternal anxiety predicted a larger attention bias for all infants. These findings provide support for attention bias as a putative early mechanism by which early markers of risk are associated with socioemotional development. (PsycINFO Database Record

  3. Inclusive Services Innovation Configuration

    ERIC Educational Resources Information Center

    Holdheide, Lynn R.; Reschly, Daniel J.

    2011-01-01

    Teacher preparation to deliver inclusive services to students with disabilities is increasingly important because of changes in law and policy emphasizing student access to, and achievement in, the general education curriculum. This innovation configuration identifies the components of inclusive services that should be incorporated in teacher…

  4. Router Security Configuration Guide

    DTIC Science & Technology

    2007-11-02

    Providing Router Security Guidance............................................................ 9 1.3. Typographic and Diagrammatic Conventions Used in this...and available software. Router Security Configuration Guide UNCLASSIFIED 10 UNCLASSIFIED Version 1.0g 1.3. Typographic and Diagrammatic... typographic conventions are used as part of presenting the examples. § Specific router and host commands are identified in the text using Courier bold

  5. Modular tokamak configuration

    SciTech Connect

    Thomson, S.L.

    1985-01-01

    This report is concerned with the modular tokamak configuration, and presents information on the following topics: modularity; external vacuum boundary; vertical maintenance; combined reactor building/biological shield with totally remote maintenance; independent TF coils; minimum TF coil bore; saddle PF coils; and heat transport system in bore.

  6. Nuclear Shuttle Logistics Configuration

    NASA Technical Reports Server (NTRS)

    1971-01-01

    This 1971 artist's concept shows the Nuclear Shuttle in both its lunar logistics configuraton and geosynchronous station configuration. As envisioned by Marshall Space Flight Center Program Development persornel, the Nuclear Shuttle would deliver payloads to lunar orbits or other destinations then return to Earth orbit for refueling and additional missions.

  7. Saturn IB Vehicle Configurations

    NASA Technical Reports Server (NTRS)

    1968-01-01

    This 1968 chart depicts the various mission configurations for the Saturn IB launch vehicle. Developed by the Marshall Space Flight Center (MSFC) as an interim vehicle in MSFC's 'building block' approach to the Saturn rocket development, the Saturn IB utilized Saturn I technology to further develop and refine the larger boosters and the Apollo spacecraft capabilities required for the marned lunar missions.

  8. Voyager: System Test Configuration

    NASA Image and Video Library

    2017-07-05

    This archival photo shows the system test configuration for Voyager on October 1, 1976. The spacecraft's 10-sided bus is visible behind the catwalk railing in the foreground. The boom that holds several of the spacecraft's science instruments arches above the railing. https://photojournal.jpl.nasa.gov/catalog/PIA21729

  9. The Bias Fallacy

    ERIC Educational Resources Information Center

    Linvill, Darren L.

    2013-01-01

    Do those who complain about liberal bias in higher education have any actionable point at all? Critics of the politicization of higher education claim that political partisanship in the classroom is pervasive and that it affects student learning. Although the existence of such partisanship has not been empirically proven, allegations of bias are…

  10. Assessing Compliance-Effect Bias in the Two Stage Least Squares Estimator

    ERIC Educational Resources Information Center

    Reardon, Sean; Unlu, Fatih; Zhu, Pei; Bloom, Howard

    2011-01-01

    The proposed paper studies the bias in the two-stage least squares, or 2SLS, estimator that is caused by the compliance-effect covariance (hereafter, the compliance-effect bias). It starts by deriving the formula for the bias in an infinite sample (i.e., in the absence of finite sample bias) under different circumstances. Specifically, it…

  11. Attention bias modification: the Emperor's new suit?

    PubMed

    Emmelkamp, Paul M G

    2012-06-25

    A series of primarily laboratory-based studies found attention bias modification in socially anxious participants to lead to reduced anxiety. It is argued that the failure to replicate the positive results of attention bias modification in the study of Carlbring et al. may be due to reasons other than the application through the Internet. A number of controlled studies failed to replicate the positive effects of attention bias modification in clinically rather than subclinically socially anxious subjects. Given the lack of robust evidence for attention bias modification in clinically socially anxious individuals, the author is inclined to consider attention bias modification as 'the Emperor's new suit'. Results achieved with regular Internet-based treatments for social anxiety disorder based on cognitive therapy and exposure methods are much better than those achieved with attention bias modification procedures delivered 'face to face' in clinically distressed participants. Given the lack of robust evidence for attention bias modification in clinical samples, there is no need yet to investigate the implementation of attention bias modification through the Internet.Please see related article: http://www.biomedcentral.com/1471-244X/12/66.

  12. Trap array configuration influences estimates and precision of black bear density and abundance.

    PubMed

    Wilton, Clay M; Puckett, Emily E; Beringer, Jeff; Gardner, Beth; Eggert, Lori S; Belant, Jerrold L

    2014-01-01

    Spatial capture-recapture (SCR) models have advanced our ability to estimate population density for wide ranging animals by explicitly incorporating individual movement. Though these models are more robust to various spatial sampling designs, few studies have empirically tested different large-scale trap configurations using SCR models. We investigated how extent of trap coverage and trap spacing affects precision and accuracy of SCR parameters, implementing models using the R package secr. We tested two trapping scenarios, one spatially extensive and one intensive, using black bear (Ursus americanus) DNA data from hair snare arrays in south-central Missouri, USA. We also examined the influence that adding a second, lower barbed-wire strand to snares had on quantity and spatial distribution of detections. We simulated trapping data to test bias in density estimates of each configuration under a range of density and detection parameter values. Field data showed that using multiple arrays with intensive snare coverage produced more detections of more individuals than extensive coverage. Consequently, density and detection parameters were more precise for the intensive design. Density was estimated as 1.7 bears per 100 km2 and was 5.5 times greater than that under extensive sampling. Abundance was 279 (95% CI = 193-406) bears in the 16,812 km2 study area. Excluding detections from the lower strand resulted in the loss of 35 detections, 14 unique bears, and the largest recorded movement between snares. All simulations showed low bias for density under both configurations. Results demonstrated that in low density populations with non-uniform distribution of population density, optimizing the tradeoff among snare spacing, coverage, and sample size is of critical importance to estimating parameters with high precision and accuracy. With limited resources, allocating available traps to multiple arrays with intensive trap spacing increased the amount of information

  13. Trap Array Configuration Influences Estimates and Precision of Black Bear Density and Abundance

    PubMed Central

    Wilton, Clay M.; Puckett, Emily E.; Beringer, Jeff; Gardner, Beth; Eggert, Lori S.; Belant, Jerrold L.

    2014-01-01

    Spatial capture-recapture (SCR) models have advanced our ability to estimate population density for wide ranging animals by explicitly incorporating individual movement. Though these models are more robust to various spatial sampling designs, few studies have empirically tested different large-scale trap configurations using SCR models. We investigated how extent of trap coverage and trap spacing affects precision and accuracy of SCR parameters, implementing models using the R package secr. We tested two trapping scenarios, one spatially extensive and one intensive, using black bear (Ursus americanus) DNA data from hair snare arrays in south-central Missouri, USA. We also examined the influence that adding a second, lower barbed-wire strand to snares had on quantity and spatial distribution of detections. We simulated trapping data to test bias in density estimates of each configuration under a range of density and detection parameter values. Field data showed that using multiple arrays with intensive snare coverage produced more detections of more individuals than extensive coverage. Consequently, density and detection parameters were more precise for the intensive design. Density was estimated as 1.7 bears per 100 km2 and was 5.5 times greater than that under extensive sampling. Abundance was 279 (95% CI = 193–406) bears in the 16,812 km2 study area. Excluding detections from the lower strand resulted in the loss of 35 detections, 14 unique bears, and the largest recorded movement between snares. All simulations showed low bias for density under both configurations. Results demonstrated that in low density populations with non-uniform distribution of population density, optimizing the tradeoff among snare spacing, coverage, and sample size is of critical importance to estimating parameters with high precision and accuracy. With limited resources, allocating available traps to multiple arrays with intensive trap spacing increased the amount of information

  14. Dynamic Airspace Configuration

    NASA Technical Reports Server (NTRS)

    Bloem, Michael J.

    2014-01-01

    In air traffic management systems, airspace is partitioned into regions in part to distribute the tasks associated with managing air traffic among different systems and people. These regions, as well as the systems and people allocated to each, are changed dynamically so that air traffic can be safely and efficiently managed. It is expected that new air traffic control systems will enable greater flexibility in how airspace is partitioned and how resources are allocated to airspace regions. In this talk, I will begin by providing an overview of some previous work and open questions in Dynamic Airspace Configuration research, which is concerned with how to partition airspace and assign resources to regions of airspace. For example, I will introduce airspace partitioning algorithms based on clustering, integer programming optimization, and computational geometry. I will conclude by discussing the development of a tablet-based tool that is intended to help air traffic controller supervisors configure airspace and controllers in current operations.

  15. Modular small hydro configuration

    NASA Astrophysics Data System (ADS)

    1981-09-01

    Smaller sites (those under 750 kilowatts) which previously were not attractive to develop using equipment intended for application at larger scale sites, were the focal point in the conception of a system which utilizes standard industrial components which are generally available within short procurement times. Such components were integrated into a development scheme for sites having 20 feet to 150 feet of head. The modular small hydro configuration maximizes the use of available components and minimizes modification of existing civil works. A key aspect of the development concept is the use of a vertical turbine multistage pump, used in the reverse mode as a hydraulic turbine. The configuration allows for automated operation and control of the hydroelectric facilities with sufficient flexibility for inclusion of potential hydroelectric sites into dispersed storage and generation (DSG) utility grid systems.

  16. Versatile composite amplifier configuration

    NASA Astrophysics Data System (ADS)

    Gift, Stephan J. G.; Maundy, Brent

    2015-06-01

    This paper describes a versatile composite amplifier in which a current feedback amplifier (CFA) drives an operational amplifier (OPA). In the conventional OPA-CFA composite amplifier, an OPA drives a CFA resulting in a composite structure that combines the DC input stability of the OPA and the high speed capability of the CFA. The proposed composite configuration combines different features of the CFA and OPA, specifically the constant bandwidth property of the CFA and the high power and high current output capacity of the OPA. The new circuit is easily implemented in the standard inverting and non-inverting configurations using commercially available devices, and the accuracy and constant bandwidth features were experimentally verified. Local feedback around the associated CFA ensures that the proposed composite amplifier possesses a higher level of bandwidth constancy than a single CFA.

  17. Implicit Social Biases in People with Autism

    PubMed Central

    Birmingham, Elina; Stanley, Damian; Nair, Remya; Adolphs, Ralph

    2015-01-01

    Implicit social biases are ubiquitous and are known to influence social behavior. A core diagnostic criterion of Autism Spectrum Disorder (ASD) is abnormal social behavior. Here we investigated the extent to which individuals with ASD might show a specific attenuation of implicit social biases, using the Implicit Association Test (IAT) across Social (gender, race) and Nonsocial (flowers/insect, shoes) categories. High-functioning adults with ASD showed intact but reduced IAT effects relative to healthy controls. Importantly, we observed no selective attenuation of implicit social (vs. nonsocial) biases in our ASD population. To extend these results, we collected data from a large online sample of the general population, and explored correlations between autistic traits and IAT effects. No associations were found between autistic traits and IAT effects for any of the categories tested in our online sample. Taken together, these results suggest that implicit social biases, as measured by the IAT, are largely intact in ASD. PMID:26386014

  18. Removing Malmquist bias from linear regressions

    NASA Technical Reports Server (NTRS)

    Verter, Frances

    1993-01-01

    Malmquist bias is present in all astronomical surveys where sources are observed above an apparent brightness threshold. Those sources which can be detected at progressively larger distances are progressively more limited to the intrinsically luminous portion of the true distribution. This bias does not distort any of the measurements, but distorts the sample composition. We have developed the first treatment to correct for Malmquist bias in linear regressions of astronomical data. A demonstration of the corrected linear regression that is computed in four steps is presented.

  19. Bounding the bias of contrastive divergence learning.

    PubMed

    Fischer, Asja; Igel, Christian

    2011-03-01

    Optimization based on k-step contrastive divergence (CD) has become a common way to train restricted Boltzmann machines (RBMs). The k-step CD is a biased estimator of the log-likelihood gradient relying on Gibbs sampling. We derive a new upper bound for this bias. Its magnitude depends on k, the number of variables in the RBM, and the maximum change in energy that can be produced by changing a single variable. The last reflects the dependence on the absolute values of the RBM parameters. The magnitude of the bias is also affected by the distance in variation between the modeled distribution and the starting distribution of the Gibbs chain.

  20. Williams configures the LMM

    NASA Image and Video Library

    2016-04-18

    ISS047e066551 (04/18/2016) --- NASA astronaut Jeff Williams configures the station’s Light Microscopy Module (LMM), a modified commercial, highly flexible, state-of-the-art light imaging microscope facility that provides researchers with powerful diagnostic hardware and software. The LMM enables novel research of microscopic phenomena in microgravity, with the capability of remotely acquiring and downloading digital images and videos across many levels of magnification.

  1. Flexible heliac configuration

    SciTech Connect

    Harris, J.H.; Cantrell, J.L.; Hender, T.C.; Carreras, B.A.; Morris, R.N.

    1985-04-01

    The addition of an l = 1 helical winding to the heliac central conductor adds a significant degree of flexibility to the configuration by making it possible to control the rotational transform and shear. Such control is essential for an experiment because the presence of low-order resonances in the rotational transform profile can cause breakup of the equilibrium magnetic surfaces. The use of the additional winding also permits reduction of the total central conductor current and can deepen the magnetic well.

  2. Fuel cell system configurations

    DOEpatents

    Kothmann, Richard E.; Cyphers, Joseph A.

    1981-01-01

    Fuel cell stack configurations having elongated polygonal cross-sectional shapes and gaskets at the peripheral faces to which flow manifolds are sealingly affixed. Process channels convey a fuel and an oxidant through longer channels, and a cooling fluid is conveyed through relatively shorter cooling passages. The polygonal structure preferably includes at least two right angles, and the faces of the stack are arranged in opposite parallel pairs.

  3. Aquarius Main Structure Configuration

    NASA Technical Reports Server (NTRS)

    Eremenko, Alexander

    2012-01-01

    The Aquarius/SAC-D Observatory is a joint US-Argentine mission to map the salinity at the ocean surface. This information is critical to improving our understanding of two major components of Earth's climate system - the water cycle and ocean circulation. By measuring ocean salinity from space, the Aquarius/SAC-D Mission will provide new insights into how the massive natural exchange of freshwater between the ocean, atmosphere and sea ice influences ocean circulation, weather and climate. Aquarius is the primary instrument on the SAC-D spacecraft. It consists of a Passive Microwave Radiometer to detect the surface emission that is used to obtain salinity and an Active Scatterometer to measure the ocean waves that affect the precision of the salinity measurement. The Aquarius Primary Structure houses instrument electronics, feed assemblies, and supports a deployable boom with a 2.5 m Reflector, and provides the structural interface to the SAC-D Spacecraft. The key challenge for the Aquarius main structure configuration is to satisfy the needs of component accommodations, ensuring that the instrument can meet all operational, pointing, environmental, and launch vehicle requirements. This paper describes the evolution of the Aquarius main structure configuration, the challenges of balancing the conflicting requirements, and the major configuration driving decisions and compromises.

  4. The ALICE Configuration Tool

    NASA Astrophysics Data System (ADS)

    Boccioli, M.; Carena, F.; Chapeland, S.; Chibante Barroso, V.; Lechman, M.; Jusko, A.; Pinazza, O.; ALICE Collaboration

    2011-12-01

    ALICE (A Large Ion Collider Experiment) is the heavy-ion detector designed to study the physics of strongly interacting matter and the quark-gluon plasma at the CERN Large Hadron Collider (LHC). It includes 18 different sub-detectors and 5 online systems, each one made of many different components and developed by different teams inside the collaboration. The operation of a large experiment over several years to collect billions of events acquired in well defined conditions requires predictability and repeatability of the experiment configuration. The logistics of the operation is also a major issue and it is mandatory to reduce the size of the shift crew needed to operate the experiment. Appropriate software tools are therefore needed to automate daily operations. This ensures minimizing human errors and maximizing the data taking time. The ALICE Configuration Tool (ACT) is ALICE first step to achieve a high level of automation, implementing automatic configuration and calibration of the sub-detectors and online systems. This presentation describes the goals and architecture of the ACT, the web-based Human Interface and the commissioning performed before the start of the collisions. It also reports on the first experiences with real use in daily operations, and finally it presents the road-map for future developments.

  5. Aquarius main structure configuration

    NASA Astrophysics Data System (ADS)

    Eremenko, A.

    The Aquarius/SAC-D Observatory is a joint US-Argentine mission to map the salinity at the ocean surface. This information is critical to improving our understanding of two major components of Earth's climate system - the water cycle and ocean circulation. By measuring ocean salinity from space, the Aquarius/SAC-D Mission will provide new insights into how the massive natural exchange of freshwater between the ocean, atmosphere and sea ice influences ocean circulation, weather and climate. Aquarius is the primary instrument on the SAC-D spacecraft. It consists of a Passive Microwave Radiometer to detect the surface emission that is used to obtain salinity and an Active Scatterometer to measure the ocean waves that affect the precision of the salinity measurement. The Aquarius Primary Structure houses instrument electronics, feed assemblies, and supports a deployable boom with a 2.5 m Reflector, and provides the structural interface to the SAC-D Spacecraft. The key challenge for the Aquarius main structure configuration is to satisfy the needs of component accommodations, ensuring that the instrument can meet all operational, pointing, environmental, and launch vehicle requirements. This paper describes the evolution of the Aquarius main structure configuration, the challenges of balancing the conflicting requirements, and the major configuration driving decisions and compromises.

  6. Biased predecision processing.

    PubMed

    Brownstein, Aaron L

    2003-07-01

    Decision makers conduct biased predecision processing when they restructure their mental representation of the decision environment to favor one alternative before making their choice. The question of whether biased predecision processing occurs has been controversial since L. Festinger (1957) maintained that it does not occur. The author reviews relevant research in sections on theories of cognitive dissonance, decision conflict, choice certainty, action control, action phases, dominance structuring, differentiation and consolidation, constructive processing, motivated reasoning, and groupthink. Some studies did not find evidence of biased predecision processing, but many did. In the Discussion section, the moderators are summarized and used to assess the theories.

  7. Introduction to Unconscious Bias

    NASA Astrophysics Data System (ADS)

    Schmelz, Joan T.

    2010-05-01

    We all have biases, and we are (for the most part) unaware of them. In general, men and women BOTH unconsciously devalue the contributions of women. This can have a detrimental effect on grant proposals, job applications, and performance reviews. Sociology is way ahead of astronomy in these studies. When evaluating identical application packages, male and female University psychology professors preferred 2:1 to hire "Brian” over "Karen” as an assistant professor. When evaluating a more experienced record (at the point of promotion to tenure), reservations were expressed four times more often when the name was female. This unconscious bias has a repeated negative effect on Karen's career. This talk will introduce the concept of unconscious bias and also give recommendations on how to address it using an example for a faculty search committee. The process of eliminating unconscious bias begins with awareness, then moves to policy and practice, and ends with accountability.

  8. Estimating Bias Error Distributions

    NASA Technical Reports Server (NTRS)

    Liu, Tian-Shu; Finley, Tom D.

    2001-01-01

    This paper formulates the general methodology for estimating the bias error distribution of a device in a measuring domain from less accurate measurements when a minimal number of standard values (typically two values) are available. A new perspective is that the bias error distribution can be found as a solution of an intrinsic functional equation in a domain. Based on this theory, the scaling- and translation-based methods for determining the bias error distribution arc developed. These methods are virtually applicable to any device as long as the bias error distribution of the device can be sufficiently described by a power series (a polynomial) or a Fourier series in a domain. These methods have been validated through computational simulations and laboratory calibration experiments for a number of different devices.

  9. Exchange-biased spin valves with perpendicular magnetic anisotropy based on (Co/Pt) multilayers

    NASA Astrophysics Data System (ADS)

    Garcia, F.; Fettar, F.; Auffret, S.; Rodmacq, B.; Dieny, B.

    2003-05-01

    We have prepared spin valves exhibiting perpendicular magnetic anisotropy [perpendicular spin valves (PSVs)] by sputtering. These PSVs associate a "free" (Co/Pt) multilayer with a "pinned" (Co/Pt)/FeMn multilayer separated by various spacer materials (Pt, Cu, Al2O3). We carried out a comprehensive study of the magnetic and magnetotransport properties of the biased multilayers and of the complete spin valves. When the number of repeats in the (Co/Pt) exchange-biased multilayer is larger than 3, the samples present 100% remnant magnetization in the perpendicular configuration. The major hysteresis cycles exhibit two well-separated loops associated with the free and the exchange-biased (Pt/Co) multilayers. When optimized, the exchange-bias field can be larger than the coercivity of the pinned layer. Metallic PSVs with Cu spacers exhibit giant magnetoresistance but the amplitude is only of the order of 1% due to significant current shunting. In contrast, perpendicularly magnetized tunnel junctions are very promising.

  10. GSC configuration management plan

    NASA Technical Reports Server (NTRS)

    Withers, B. Edward

    1990-01-01

    The tools and methods used for the configuration management of the artifacts (including software and documentation) associated with the Guidance and Control Software (GCS) project are described. The GCS project is part of a software error studies research program. Three implementations of GCS are being produced in order to study the fundamental characteristics of the software failure process. The Code Management System (CMS) is used to track and retrieve versions of the documentation and software. Application of the CMS for this project is described and the numbering scheme is delineated for the versions of the project artifacts.

  11. Beyond Kaiser bias: mildly non-linear two-point statistics of densities in distant spheres

    NASA Astrophysics Data System (ADS)

    Uhlemann, C.; Codis, S.; Kim, J.; Pichon, C.; Bernardeau, F.; Pogosyan, D.; Park, C.; L'Huillier, B.

    2017-04-01

    We present simple parameter-free analytic bias functions for the two-point correlation of densities in spheres at large separation. These bias functions generalize the so-called Kaiser bias to the mildly non-linear regime for arbitrary density contrasts and grow as b(ρ) - b(1) ∝ (1 - ρ-13/21)ρ1 + n/3 with b(1) = -4/21 - n/3 for a power-law initial spectrum with index n. We carry out the derivation in the context of large-deviation statistics while relying on the spherical collapse model. We use a logarithmic transformation that provides a saddle-point approximation that is valid for the whole range of densities and show its accuracy against the 30 Gpc cube state-of-the-art Horizon Run 4 simulation. Special configurations of two concentric spheres that allow us to identify peaks are employed to obtain the conditional bias and a proxy for the BBKS extremum correlation functions. These analytic bias functions should be used jointly with extended perturbation theory to predict two-point clustering statistics as they capture the non-linear regime of structure formation at the per cent level down to scales of about 10 Mpc h-1 at redshift 0. Conversely, the joint statistics also provide us with optimal dark matter two-point correlation estimates that can be applied either universally to all spheres or to a restricted set of biased (over- or underdense) pairs. Based on a simple fiducial survey, we show that the variance of this estimator is reduced by five times relative to the traditional sample estimator for the two-point function. Extracting more information from correlations of different types of objects should prove essential in the context of upcoming surveys like Euclid, DESI and WFIRST.

  12. Ames Optimized TCA Configuration

    NASA Technical Reports Server (NTRS)

    Cliff, Susan E.; Reuther, James J.; Hicks, Raymond M.

    1999-01-01

    Configuration design at Ames was carried out with the SYN87-SB (single block) Euler code using a 193 x 49 x 65 C-H grid. The Euler solver is coupled to the constrained (NPSOL) and the unconstrained (QNMDIF) optimization packages. Since the single block grid is able to model only wing-body configurations, the nacelle/diverter effects were included in the optimization process by SYN87's option to superimpose the nacelle/diverter interference pressures on the wing. These interference pressures were calculated using the AIRPLANE code. AIRPLANE is an Euler solver that uses a unstructured tetrahedral mesh and is capable of computations about arbitrary complete configurations. In addition, the buoyancy effects of the nacelle/diverters were also included in the design process by imposing the pressure field obtained during the design process onto the triangulated surfaces of the nacelle/diverter mesh generated by AIRPLANE. The interference pressures and nacelle buoyancy effects are added to the final forces after each flow field calculation. Full details of the (recently enhanced) ghost nacelle capability are given in a related talk. The pseudo nacelle corrections were greatly improved during this design cycle. During the Ref H and Cycle 1 design activities, the nacelles were only translated and pitched. In the cycle 2 design effort the nacelles can translate vertically, and pitch to accommodate the changes in the lower surface geometry. The diverter heights (between their leading and trailing edges) were modified during design as the shape of the lower wing changed, with the drag of the diverter changing accordingly. Both adjoint and finite difference gradients were used during optimization. The adjoint-based gradients were found to give good direction in the design space for configurations near the starting point, but as the design approached a minimum, the finite difference gradients were found to be more accurate. Use of finite difference gradients was limited by the

  13. Ames Optimized TCA Configuration

    NASA Technical Reports Server (NTRS)

    Cliff, Susan E.; Reuther, James J.; Hicks, Raymond M.

    1999-01-01

    Configuration design at Ames was carried out with the SYN87-SB (single block) Euler code using a 193 x 49 x 65 C-H grid. The Euler solver is coupled to the constrained (NPSOL) and the unconstrained (QNMDIF) optimization packages. Since the single block grid is able to model only wing-body configurations, the nacelle/diverter effects were included in the optimization process by SYN87's option to superimpose the nacelle/diverter interference pressures on the wing. These interference pressures were calculated using the AIRPLANE code. AIRPLANE is an Euler solver that uses a unstructured tetrahedral mesh and is capable of computations about arbitrary complete configurations. In addition, the buoyancy effects of the nacelle/diverters were also included in the design process by imposing the pressure field obtained during the design process onto the triangulated surfaces of the nacelle/diverter mesh generated by AIRPLANE. The interference pressures and nacelle buoyancy effects are added to the final forces after each flow field calculation. Full details of the (recently enhanced) ghost nacelle capability are given in a related talk. The pseudo nacelle corrections were greatly improved during this design cycle. During the Ref H and Cycle 1 design activities, the nacelles were only translated and pitched. In the cycle 2 design effort the nacelles can translate vertically, and pitch to accommodate the changes in the lower surface geometry. The diverter heights (between their leading and trailing edges) were modified during design as the shape of the lower wing changed, with the drag of the diverter changing accordingly. Both adjoint and finite difference gradients were used during optimization. The adjoint-based gradients were found to give good direction in the design space for configurations near the starting point, but as the design approached a minimum, the finite difference gradients were found to be more accurate. Use of finite difference gradients was limited by the

  14. SIM Configuration Evolution

    NASA Technical Reports Server (NTRS)

    Aaron, Kim M.

    2000-01-01

    The Space Interferometry Mission (SIM) is a space-based 10 m baseline Michelson interferometer. Planned for launch in 2005 aboard a Delta III launch vehicle, or equivalent, its primary objective is to measure the positions of stars and other celestial objects with an unprecedented accuracy of 4 micro arc seconds. With such an instrument, tremendous advancement can be expected in our understanding of stellar and galactic dynamics. Using triangulation from opposite sides of the orbit around the sun (i.e. by using parallax) one can measure the distance to any observable object in our galaxy. By directly measuring the orbital wobble of nearby stars, the mass and orbit of planets can be determined over a wide range of parameters. The distribution of velocity within nearby galaxies will be measurable. Observations of these and other objects will improve the calibration of distance estimators by more than an order of magnitude. This will permit a much better determination of the Hubble Constant as well as improving our overall understanding of the evolution of the universe. SIM has undergone several transformations, especially over the past year and a half since the start of Phase A. During this phase of a project, it is desirable to perform system-level trade studies, so the substantial evolution of the design that has occurred is quite appropriate. Part of the trade-off process has addressed two major underlying architectures: SIM Classic; and Son of SIM. The difference between these two architectures is related to the overall arrangement of the optical elements and the associated metrology system. Several different configurations have been developed for each architecture. Each configuration is the result of design choices that are influenced by many competing considerations. Some of the more important aspects will be discussed. The Space Interferometry Mission has some extremely challenging goals: millikelvin thermal stability, nanometer stabilization of optics

  15. Interface Circuit for Vibration Energy Harvesting with Adjustable Bias Voltage

    NASA Astrophysics Data System (ADS)

    Wei, J.; Lefeuvre, E.; Mathias, H.; Costa, F.

    2015-12-01

    This paper presents a new interface circuit for electrostatic vibration energy harvesting with adjustable bias voltage. An electronic switch is used to modify the circuit configuration so that the harvested energy increases the voltage across a biasing capacitor. Decrease of this biasing capacitor voltage occurs naturally due to the circuit imperfections. Such a control of the bias voltage enables to adjust the amount of energy converted by the variable capacitor on each cycle. This feature can be used to optimize the mechanical damping induced by the energy conversion process in order to maximize the harvested power. Another feature of this interface circuit is that it is capable to get high bias voltage whatever the battery voltage with low energy loss.

  16. Affective forecasting bias in preschool children.

    PubMed

    Gautam, Shalini; Bulley, Adam; von Hippel, William; Suddendorf, Thomas

    2017-03-10

    Adults are capable of predicting their emotional reactions to possible future events. Nevertheless, they systematically overestimate the intensity of their future emotional reactions relative to how they feel when these events actually occur. The developmental origin of this "intensity bias" has not yet been examined. Two studies were conducted to test the intensity bias in preschool children. In the first study, 5-year-olds (N=30) predicted how they would feel if they won or lost various games. Comparisons with subsequent self-reported feelings indicated that participants overestimated how sad they would feel to lose the games but did not overestimate their happiness from winning. The second study replicated this effect in another sample of 5-year-olds (n=34) and also found evidence of an intensity bias in 4-year-olds (n=30). These findings provide the first evidence of a negative intensity bias in affective forecasting among young children.

  17. Configurations of Common Childhood Psychosocial Risk Factors

    ERIC Educational Resources Information Center

    Copeland, William; Shanahan, Lilly; Costello, E. Jane; Angold, Adrian

    2009-01-01

    Background: Co-occurrence of psychosocial risk factors is commonplace, but little is known about psychiatrically-predictive configurations of psychosocial risk factors. Methods: Latent class analysis (LCA) was applied to 17 putative psychosocial risk factors in a representative population sample of 920 children ages 9 to 17. The resultant class…

  18. Configurations of Common Childhood Psychosocial Risk Factors

    ERIC Educational Resources Information Center

    Copeland, William; Shanahan, Lilly; Costello, E. Jane; Angold, Adrian

    2009-01-01

    Background: Co-occurrence of psychosocial risk factors is commonplace, but little is known about psychiatrically-predictive configurations of psychosocial risk factors. Methods: Latent class analysis (LCA) was applied to 17 putative psychosocial risk factors in a representative population sample of 920 children ages 9 to 17. The resultant class…

  19. Study of the Dependence on Magnetic Field and Bias Voltage of an AC-Biased TES Microcalorimeter

    NASA Technical Reports Server (NTRS)

    Bandler, Simon

    2011-01-01

    At SRON we are studying the performance of a Goddard Space Flight Center single pixel TES microcalorimeter operated in the AC bias configuration. For x-ray photons at 6keV the AC biased pixel shows a best energy resolution of 3.7eV, which is about a factor of 2 worse than the energy resolution observed in identical DC-biased pixels. To better understand the reasons of this discrepancy, we investigated the detector performance as a function of temperature, bias working point and applied magnetic field. A strong periodic dependence of the detector noise on the TES AC bias voltage is measured. We discuss the results in the framework of the recent weak-link behaviour observed inTES microcalorimeters.

  20. Inductrack magnet configuration

    DOEpatents

    Post, Richard Freeman

    2003-10-14

    A magnet configuration comprising a pair of Halbach arrays magnetically and structurally connected together are positioned with respect to each other so that a first component of their fields substantially cancels at a first plane between them, and a second component of their fields substantially adds at this first plane. A track of windings is located between the pair of Halbach arrays and a propulsion mechanism is provided for moving the pair of Halbach arrays along the track. When the pair of Halbach arrays move along the track and the track is not located at the first plane, a current is induced in the windings and a restoring force is exerted on the pair of Halbach arrays.

  1. Inductrack magnet configuration

    DOEpatents

    Post, Richard Freeman

    2003-12-16

    A magnet configuration comprising a pair of Halbach arrays magnetically and structurally connected together are positioned with respect to each other so that a first component of their fields substantially cancels at a first plane between them, and a second component of their fields substantially adds at this first plane. A track of windings is located between the pair of Halbach arrays and a propulsion mechanism is provided for moving the pair of Halbach arrays along the track. When the pair of Halbach arrays move along the track and the track is not located at the first plane, a current is induced in the windings and a restoring force is exerted on the pair of Halbach arrays.

  2. Power converter connection configuration

    SciTech Connect

    Beihoff, Bruce C.; Kehl, Dennis L.; Gettelfinger, Lee A.; Kaishian, Steven C.; Phillips, Mark G.; Radosevich, Lawrence D.

    2008-11-11

    EMI shielding is provided for power electronics circuits and the like via a direct-mount reference plane support and shielding structure. The thermal support may receive one or more power electronic circuits. The support may aid in removing heat from the circuits through fluid circulating through the support. The support forms a shield from both external EMI/RFI and from interference generated by operation of the power electronic circuits. Features may be provided to permit and enhance connection of the circuitry to external circuitry, such as improved terminal configurations. Modular units may be assembled that may be coupled to electronic circuitry via plug-in arrangements or through interface with a backplane or similar mounting and interconnecting structures.

  3. Configurable Aperture Space Telescope

    NASA Technical Reports Server (NTRS)

    Ennico, Kimberly; Vassigh, Kenny; Bendek, Selman; Young, Zion W; Lynch, Dana H.

    2015-01-01

    In December 2014, we were awarded Center Innovation Fund to evaluate an optical and mechanical concept for a novel implementation of a segmented telescope based on modular, interconnected small sats (satlets). The concept is called CAST, a Configurable Aperture Space Telescope. With a current TRL is 2 we will aim to reach TLR 3 in Sept 2015 by demonstrating a 2x2 mirror system to validate our optical model and error budget, provide strawman mechanical architecture and structural damping analyses, and derive future satlet-based observatory performance requirements. CAST provides an alternative access to visible andor UV wavelength space telescope with 1-meter or larger aperture for NASA SMD Astrophysics and Planetary Science community after the retirement of HST.

  4. Software Configurable Multichannel Transceiver

    NASA Technical Reports Server (NTRS)

    Freudinger, Lawrence C.; Cornelius, Harold; Hickling, Ron; Brooks, Walter

    2009-01-01

    Emerging test instrumentation and test scenarios increasingly require network communication to manage complexity. Adapting wireless communication infrastructure to accommodate challenging testing needs can benefit from reconfigurable radio technology. A fundamental requirement for a software-definable radio system is independence from carrier frequencies, one of the radio components that to date has seen only limited progress toward programmability. This paper overviews an ongoing project to validate the viability of a promising chipset that performs conversion of radio frequency (RF) signals directly into digital data for the wireless receiver and, for the transmitter, converts digital data into RF signals. The Software Configurable Multichannel Transceiver (SCMT) enables four transmitters and four receivers in a single unit the size of a commodity disk drive, programmable for any frequency band between 1 MHz and 6 GHz.

  5. Configurable Aperture Space Telescope

    NASA Technical Reports Server (NTRS)

    Ennico, Kimberly; Bendek, Eduardo

    2015-01-01

    In December 2014, we were awarded Center Innovation Fund to evaluate an optical and mechanical concept for a novel implementation of a segmented telescope based on modular, interconnected small sats (satlets). The concept is called CAST, a Configurable Aperture Space Telescope. With a current TRL is 2 we will aim to reach TLR 3 in Sept 2015 by demonstrating a 2x2 mirror system to validate our optical model and error budget, provide straw man mechanical architecture and structural damping analyses, and derive future satlet-based observatory performance requirements. CAST provides an alternative access to visible and/or UV wavelength space telescope with 1-meter or larger aperture for NASA SMD Astrophysics and Planetary Science community after the retirement of HST

  6. SASSI system software configuration

    SciTech Connect

    Weiner, E.O.

    1994-08-01

    The SASSI (System for Analysis for Soil-Structure Interaction) computer program was obtained by WHC from the University of California at Berkeley for seismic structural analysis of complex embedded building configurations. SASSI was developed in the 1980`s by a team of doctoral students under the direction of Prof. J. Lysmer. The program treats three-dimensional soil-structure interaction problems with the flexible volume substructuring method. In the 1970`s, the same organization developed the FLUSH program, which has achieved widespread international usage in the seismic analysis of structures. SASSI consists of nine modules, each of which are to be run as a separate execution. The SASSI source code, dated 1989 and identified as a Cray version, was put up on the RL Cray XM/232 Unicos system in 1991. That system was removed at the end of 1993, and SASSI is now installed on the LANL Cray YMP systems.

  7. Distinguishing Selection Bias and Confounding Bias in Comparative Effectiveness Research.

    PubMed

    Haneuse, Sebastien

    2016-04-01

    Comparative effectiveness research (CER) aims to provide patients and physicians with evidence-based guidance on treatment decisions. As researchers conduct CER they face myriad challenges. Although inadequate control of confounding is the most-often cited source of potential bias, selection bias that arises when patients are differentially excluded from analyses is a distinct phenomenon with distinct consequences: confounding bias compromises internal validity, whereas selection bias compromises external validity. Despite this distinction, however, the label "treatment-selection bias" is being used in the CER literature to denote the phenomenon of confounding bias. Motivated by an ongoing study of treatment choice for depression on weight change over time, this paper formally distinguishes selection and confounding bias in CER. By formally distinguishing selection and confounding bias, this paper clarifies important scientific, design, and analysis issues relevant to ensuring validity. First is that the 2 types of biases may arise simultaneously in any given study; even if confounding bias is completely controlled, a study may nevertheless suffer from selection bias so that the results are not generalizable to the patient population of interest. Second is that the statistical methods used to mitigate the 2 biases are themselves distinct; methods developed to control one type of bias should not be expected to address the other. Finally, the control of selection and confounding bias will often require distinct covariate information. Consequently, as researchers plan future studies of comparative effectiveness, care must be taken to ensure that all data elements relevant to both confounding and selection bias are collected.

  8. Biases in Visual, Auditory, and Audiovisual Perception of Space

    PubMed Central

    Odegaard, Brian; Wozny, David R.; Shams, Ladan

    2015-01-01

    Localization of objects and events in the environment is critical for survival, as many perceptual and motor tasks rely on estimation of spatial location. Therefore, it seems reasonable to assume that spatial localizations should generally be accurate. Curiously, some previous studies have reported biases in visual and auditory localizations, but these studies have used small sample sizes and the results have been mixed. Therefore, it is not clear (1) if the reported biases in localization responses are real (or due to outliers, sampling bias, or other factors), and (2) whether these putative biases reflect a bias in sensory representations of space or a priori expectations (which may be due to the experimental setup, instructions, or distribution of stimuli). Here, to address these questions, a dataset of unprecedented size (obtained from 384 observers) was analyzed to examine presence, direction, and magnitude of sensory biases, and quantitative computational modeling was used to probe the underlying mechanism(s) driving these effects. Data revealed that, on average, observers were biased towards the center when localizing visual stimuli, and biased towards the periphery when localizing auditory stimuli. Moreover, quantitative analysis using a Bayesian Causal Inference framework suggests that while pre-existing spatial biases for central locations exert some influence, biases in the sensory representations of both visual and auditory space are necessary to fully explain the behavioral data. How are these opposing visual and auditory biases reconciled in conditions in which both auditory and visual stimuli are produced by a single event? Potentially, the bias in one modality could dominate, or the biases could interact/cancel out. The data revealed that when integration occurred in these conditions, the visual bias dominated, but the magnitude of this bias was reduced compared to unisensory conditions. Therefore, multisensory integration not only improves the

  9. Attention bias modification training under working memory load increases the magnitude of change in attentional bias.

    PubMed

    Clarke, Patrick J F; Branson, Sonya; Chen, Nigel T M; Van Bockstaele, Bram; Salemink, Elske; MacLeod, Colin; Notebaert, Lies

    2017-12-01

    Attention bias modification (ABM) procedures have shown promise as a therapeutic intervention, however current ABM procedures have proven inconsistent in their ability to reliably achieve the requisite change in attentional bias needed to produce emotional benefits. This highlights the need to better understand the precise task conditions that facilitate the intended change in attention bias in order to realise the therapeutic potential of ABM procedures. Based on the observation that change in attentional bias occurs largely outside conscious awareness, the aim of the current study was to determine if an ABM procedure delivered under conditions likely to preclude explicit awareness of the experimental contingency, via the addition of a working memory load, would contribute to greater change in attentional bias. Bias change was assessed among 122 participants in response to one of four ABM tasks given by the two experimental factors of ABM training procedure delivered either with or without working memory load, and training direction of either attend-negative or avoid-negative. Findings revealed that avoid-negative ABM procedure under working memory load resulted in significantly greater reductions in attentional bias compared to the equivalent no-load condition. The current findings will require replication with clinical samples to determine the utility of the current task for achieving emotional benefits. These present findings are consistent with the position that the addition of a working memory load may facilitate change in attentional bias in response to an ABM training procedure. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Double propensity-score adjustment: A solution to design bias or bias due to incomplete matching.

    PubMed

    Austin, Peter C

    2017-02-01

    Propensity-score matching is frequently used to reduce the effects of confounding when using observational data to estimate the effects of treatments. Matching allows one to estimate the average effect of treatment in the treated. Rosenbaum and Rubin coined the term "bias due to incomplete matching" to describe the bias that can occur when some treated subjects are excluded from the matched sample because no appropriate control subject was available. The presence of incomplete matching raises important questions around the generalizability of estimated treatment effects to the entire population of treated subjects. We describe an analytic solution to address the bias due to incomplete matching. Our method is based on using optimal or nearest neighbor matching, rather than caliper matching (which frequently results in the exclusion of some treated subjects). Within the sample matched on the propensity score, covariate adjustment using the propensity score is then employed to impute missing potential outcomes under lack of treatment for each treated subject. Using Monte Carlo simulations, we found that the proposed method resulted in estimates of treatment effect that were essentially unbiased. This method resulted in decreased bias compared to caliper matching alone and compared to either optimal matching or nearest neighbor matching alone. Caliper matching alone resulted in design bias or bias due to incomplete matching, while optimal matching or nearest neighbor matching alone resulted in bias due to residual confounding. The proposed method also tended to result in estimates with decreased mean squared error compared to when caliper matching was used.

  11. Double propensity-score adjustment: A solution to design bias or bias due to incomplete matching

    PubMed Central

    2016-01-01

    Propensity-score matching is frequently used to reduce the effects of confounding when using observational data to estimate the effects of treatments. Matching allows one to estimate the average effect of treatment in the treated. Rosenbaum and Rubin coined the term “bias due to incomplete matching” to describe the bias that can occur when some treated subjects are excluded from the matched sample because no appropriate control subject was available. The presence of incomplete matching raises important questions around the generalizability of estimated treatment effects to the entire population of treated subjects. We describe an analytic solution to address the bias due to incomplete matching. Our method is based on using optimal or nearest neighbor matching, rather than caliper matching (which frequently results in the exclusion of some treated subjects). Within the sample matched on the propensity score, covariate adjustment using the propensity score is then employed to impute missing potential outcomes under lack of treatment for each treated subject. Using Monte Carlo simulations, we found that the proposed method resulted in estimates of treatment effect that were essentially unbiased. This method resulted in decreased bias compared to caliper matching alone and compared to either optimal matching or nearest neighbor matching alone. Caliper matching alone resulted in design bias or bias due to incomplete matching, while optimal matching or nearest neighbor matching alone resulted in bias due to residual confounding. The proposed method also tended to result in estimates with decreased mean squared error compared to when caliper matching was used. PMID:25038071

  12. Optically biased laser gyro

    SciTech Connect

    Anderson, D.Z.; Chow, W.W.; Scully, M.O.; Sanders, V.E.

    1980-10-01

    We describe a four-mode ring laser that exhibits none of the mode-locking characteristics that plague laser gyros. This laser is characterized by a bias that changes sign with a change in the direction of rotation and prevents the counterpropagating modes from locking. A theoretical analysis explaining the experimental results is outlined.

  13. A significant bias

    NASA Astrophysics Data System (ADS)

    Eades, Alwyn

    2013-09-01

    While I do not wish to belittle the unfortunate conclusions that may be drawn from your news article "Gender bias judges research by women more critically" (May p12), I do want to comment on the way the article is presented.

  14. Sex Bias in Children.

    ERIC Educational Resources Information Center

    Zalk, Sue Rosenberg; And Others

    This study investigated children's sex biased attitudes as a function of the sex, age, and race of the child as well as a geographical-SES factor. Two attitudes were measured on a 55-item questionnaire: Sex Pride (attributing positive characteristics to a child of the same sex) and Sex Prejudice (attributing negative characteristics to a child of…

  15. Own Variety Bias

    PubMed Central

    García, Andrea Ariza

    2015-01-01

    In a language identification task, native Belgian French and native Swiss French speakers identified French from France as their own variety. However, Canadian French was not subject to this bias. Canadian and French listeners didn’t claim a different variety as their own. PMID:27648211

  16. Sampling artifacts from the use of denuder tubes with glycerol based coatings in the measurement of atmospheric particulate matter.

    PubMed

    Finn, D; Rumburg, B; Claiborn, C; Bamesberger, L; Siems, W F; Koenig, J; Larson, T; Norris, G

    2001-01-01

    Chemical speciation studies use sampling configurations that often require the deployment of denuder tubes of various types to measure certain species or control particulate sampling artifacts. Concurrent sets of measurements on Teflon membrane and quartz filters in specific sampling configurations were used to evaluate the potential influence of denuder tubes with glycerol-based coatings on particulate mass and carbon measurements on downstream filters. Positive biases were observed in the measurement of gravimetric mass and carbon on Teflon and quartz filters, respectively, downstream of sodium carbonate/ glycerol and citric acid/glycerol coated denuder tubes relative to those without upstream denuder tubes. The magnitude of the bias is dependent on the level of ambient particulate loading.

  17. Modeling confirmation bias and polarization

    PubMed Central

    Del Vicario, Michela; Scala, Antonio; Caldarelli, Guido; Stanley, H. Eugene; Quattrociocchi, Walter

    2017-01-01

    Online users tend to select claims that adhere to their system of beliefs and to ignore dissenting information. Confirmation bias, indeed, plays a pivotal role in viral phenomena. Furthermore, the wide availability of content on the web fosters the aggregation of likeminded people where debates tend to enforce group polarization. Such a configuration might alter the public debate and thus the formation of the public opinion. In this paper we provide a mathematical model to study online social debates and the related polarization dynamics. We assume the basic updating rule of the Bounded Confidence Model (BCM) and we develop two variations a) the Rewire with Bounded Confidence Model (RBCM), in which discordant links are broken until convergence is reached; and b) the Unbounded Confidence Model, under which the interaction among discordant pairs of users is allowed even with a negative feedback, either with the rewiring step (RUCM) or without it (UCM). From numerical simulations we find that the new models (UCM and RUCM), unlike the BCM, are able to explain the coexistence of two stable final opinions, often observed in reality. Lastly, we present a mean field approximation of the newly introduced models. PMID:28074874

  18. Modeling confirmation bias and polarization

    NASA Astrophysics Data System (ADS)

    Del Vicario, Michela; Scala, Antonio; Caldarelli, Guido; Stanley, H. Eugene; Quattrociocchi, Walter

    2017-01-01

    Online users tend to select claims that adhere to their system of beliefs and to ignore dissenting information. Confirmation bias, indeed, plays a pivotal role in viral phenomena. Furthermore, the wide availability of content on the web fosters the aggregation of likeminded people where debates tend to enforce group polarization. Such a configuration might alter the public debate and thus the formation of the public opinion. In this paper we provide a mathematical model to study online social debates and the related polarization dynamics. We assume the basic updating rule of the Bounded Confidence Model (BCM) and we develop two variations a) the Rewire with Bounded Confidence Model (RBCM), in which discordant links are broken until convergence is reached; and b) the Unbounded Confidence Model, under which the interaction among discordant pairs of users is allowed even with a negative feedback, either with the rewiring step (RUCM) or without it (UCM). From numerical simulations we find that the new models (UCM and RUCM), unlike the BCM, are able to explain the coexistence of two stable final opinions, often observed in reality. Lastly, we present a mean field approximation of the newly introduced models.

  19. Investigating bias in squared regression structure coefficients.

    PubMed

    Nimon, Kim F; Zientek, Linda R; Thompson, Bruce

    2015-01-01

    The importance of structure coefficients and analogs of regression weights for analysis within the general linear model (GLM) has been well-documented. The purpose of this study was to investigate bias in squared structure coefficients in the context of multiple regression and to determine if a formula that had been shown to correct for bias in squared Pearson correlation coefficients and coefficients of determination could be used to correct for bias in squared regression structure coefficients. Using data from a Monte Carlo simulation, this study found that squared regression structure coefficients corrected with Pratt's formula produced less biased estimates and might be more accurate and stable estimates of population squared regression structure coefficients than estimates with no such corrections. While our findings are in line with prior literature that identified multicollinearity as a predictor of bias in squared regression structure coefficients but not coefficients of determination, the findings from this study are unique in that the level of predictive power, number of predictors, and sample size were also observed to contribute bias in squared regression structure coefficients.

  20. Investigating bias in squared regression structure coefficients

    PubMed Central

    Nimon, Kim F.; Zientek, Linda R.; Thompson, Bruce

    2015-01-01

    The importance of structure coefficients and analogs of regression weights for analysis within the general linear model (GLM) has been well-documented. The purpose of this study was to investigate bias in squared structure coefficients in the context of multiple regression and to determine if a formula that had been shown to correct for bias in squared Pearson correlation coefficients and coefficients of determination could be used to correct for bias in squared regression structure coefficients. Using data from a Monte Carlo simulation, this study found that squared regression structure coefficients corrected with Pratt's formula produced less biased estimates and might be more accurate and stable estimates of population squared regression structure coefficients than estimates with no such corrections. While our findings are in line with prior literature that identified multicollinearity as a predictor of bias in squared regression structure coefficients but not coefficients of determination, the findings from this study are unique in that the level of predictive power, number of predictors, and sample size were also observed to contribute bias in squared regression structure coefficients. PMID:26217273

  1. Incremental full configuration interaction

    NASA Astrophysics Data System (ADS)

    Zimmerman, Paul M.

    2017-03-01

    The incremental expansion provides a polynomial scaling method for computing electronic correlation energies. This article details a new algorithm and implementation for the incremental expansion of full configuration interaction (FCI), called iFCI. By dividing the problem into n-body interaction terms, accurate correlation energies can be recovered at low n in a highly parallel computation. Additionally, relatively low-cost approximations are possible in iFCI by solving for each incremental energy to within a specified threshold. Herein, systematic tests show that FCI-quality energies can be asymptotically reached for cases where dynamic correlation is dominant as well as where static correlation is vital. To further reduce computational costs and allow iFCI to reach larger systems, a select-CI approach (heat-bath CI) requiring two parameters is incorporated. Finally, iFCI provides the first estimate of FCI energies for hexatriene with a polarized double zeta basis set, which has 32 electrons correlated in 118 orbitals, corresponding to a FCI dimension of over 1038.

  2. Total equipment parts configuration

    SciTech Connect

    Ferrare, J.; Panzani, F.

    1989-01-01

    Florida Power Lights's (FP L's) Turkey Point units were built prior to the establishment of American Society of Mechanical Engineers' Sec. III requirements. Since that time, FP L has voluntarily committed to procuring some spare and replacement parts in compliance with the ordering requirements of ASME Sec. III. New subsystems were designed according to ASME Sec. III requirements. In 1978, 10CFR21 of the Code of Federal Regulations was federally mandated. Environmental qualification concerns and the Three Mile Island incident further complicated the stocking and ordering of spare and replacement parts. Turkey Point assembled a team of quality assurance, quality control, and engineering people and obtained permission to directly access the store department computer so that catalog descriptions could be quickly made available for use by the plant. The total equipment parts configuration (TEPC) system was designed and developed under the direction of the procurement document review team at the Turkey Point nuclear plant. The system is a network of related computer data bases that identifies the equipment at the plant. The equipment (or components that make up a piece of equipment) is identified by a tag/component code system. Each component is further broken down by the manufacturer's parts list or bill of material. A description of the data available to the user, the ways these data can be accessed and displayed, and a description of the data bases and their relation to each other are summarized in this paper.

  3. Selecting a Sample

    ERIC Educational Resources Information Center

    Ritter, Lois A., Ed.; Sue, Valerie M., Ed.

    2007-01-01

    This chapter provides an overview of sampling methods that are appropriate for conducting online surveys. The authors review some of the basic concepts relevant to online survey sampling, present some probability and nonprobability techniques for selecting a sample, and briefly discuss sample size determination and nonresponse bias. Although some…

  4. A Lack of Left Visual Field Bias when Individuals with Autism Process Faces

    ERIC Educational Resources Information Center

    Dundas, Eva M.; Best, Catherine A.; Minshew, Nancy J.; Strauss, Mark S.

    2012-01-01

    It has been established that typically developing individuals have a bias to attend to facial information in the left visual field (LVF) more than in the right visual field. This bias is thought to arise from the right hemisphere's advantage for processing facial information, with evidence suggesting it to be driven by the configural demands of…

  5. A Lack of Left Visual Field Bias when Individuals with Autism Process Faces

    ERIC Educational Resources Information Center

    Dundas, Eva M.; Best, Catherine A.; Minshew, Nancy J.; Strauss, Mark S.

    2012-01-01

    It has been established that typically developing individuals have a bias to attend to facial information in the left visual field (LVF) more than in the right visual field. This bias is thought to arise from the right hemisphere's advantage for processing facial information, with evidence suggesting it to be driven by the configural demands of…

  6. Hubble Space Telescope Configuration

    NASA Technical Reports Server (NTRS)

    1980-01-01

    This illustration shows the Hubble Space Telescope's (HST's) major configuration elements. The spacecraft has three interacting systems: The Support System Module (SSM), an outer structure that houses the other systems and provides services such as power, communication, and control; The Optical Telescope Assembly (OTA), which collects and concentrates the incoming light in the focal plane for use by the Scientific Instruments (SI); and five SIs. The SI Control and Data Handling (CDH) unit controls the five SI's, four that are housed in an aft section focal plane structure and one that is placed along the circumference of the spacecraft. The purpose of the HST, the most complex and sensitive optical telescope ever made, is to study the cosmos from a low-Earth orbit. By placing the telescope in space, astronomers are able to collect data that is free of the Earth's atmosphere. The HST detects objects 25 times fainter than the dimmest objects seen from Earth and provides astronomers with an observable universe 250 times larger than visible from ground-based telescopes, perhaps as far away as 14 billion light-years. The HST views galaxies, stars, planets, comets, possibly other solar systems, and even unusual phenomena such as quasars, with 10 times the clarity of ground-based telescopes. The HST was deployed from the Space Shuttle Discovery (STS-31 mission) into Earth orbit in April 1990. The Marshall Space Flight Center had responsibility for design, development, and construction of the HST. The Perkin-Elmer Corporation, in Danbury, Cornecticut, developed the optical system and guidance sensors. The Lockheed Missile and Space Company of Sunnyvale, California produced the protective outer shroud and spacecraft systems, and assembled and tested the finished telescope.

  7. Parametric study of statistical bias in laser Doppler velocimetry

    NASA Technical Reports Server (NTRS)

    Gould, Richard D.; Stevenson, Warren H.; Thompson, H. Doyle

    1989-01-01

    Analytical studies have often assumed that LDV velocity bias depends on turbulence intensity in conjunction with one or more characteristic time scales, such as the time between validated signals, the time between data samples, and the integral turbulence time-scale. These parameters are presently varied independently, in an effort to quantify the biasing effect. Neither of the post facto correction methods employed is entirely accurate. The mean velocity bias error is found to be nearly independent of data validation rate.

  8. Berkson’s bias, selection bias, and missing data

    PubMed Central

    Westreich, Daniel

    2011-01-01

    While Berkson’s bias is widely recognized in the epidemiologic literature, it remains underappreciated as a model of both selection bias and bias due to missing data. Simple causal diagrams and 2×2 tables illustrate how Berkson’s bias connects to collider bias and selection bias more generally, and show the strong analogies between Berksonian selection bias and bias due to missing data. In some situations, considerations of whether data are missing at random or missing not at random is less important than the causal structure of the missing-data process. While dealing with missing data always relies on strong assumptions about unobserved variables, the intuitions built with simple examples can provide a better understanding of approaches to missing data in real-world situations. PMID:22081062

  9. Recursion Formulas of Central Configurations.

    NASA Astrophysics Data System (ADS)

    Tien, Fangcheng

    1993-01-01

    This paper analyzes central configurations which are special configurations leading to homothetic solutions of the n-body problem. For the planar central configurations, these solutions also provide periodic solutions of the n-body problem. Chapter 1 defines the problem and provides an overview of the area. There is historical interest in knowing the total number of these central configurations. For n >= 4 the problem remains unsolved. Furthermore, a different mass ratio between the n bodies will produce a different total number of central configurations. This paper will provide the total number of central configurations which has a special mass ratio. For the planar central configurations the total number of central configurations grows at the speed n!2n, and the three dimensional case is n!3^{n }. Chapters 2, 3 and 5 give details and proofs of the analytical continuation method. This method begins with three bodies, then creates the central configurations with four bodies with one small mass, using the implicit function theorem. If the process is repeated, the total number of central configurations for any n-body problem may be calculated, provided (n-3) masses are sufficiently small. In Chapters 4 and 7, the formulas are derived for the total number of central configurations of the n-body problem with special mass ratio (m _1,m_2,m_3,epsilon_1, ...,epsilonn) in both planar and three-dimensional cases. Examples of formulas provided are: n!(2^{n+1} + 1) , n!((n^2 - n + 4)2^{n+1 } - n - 7), and (n!/6) ((n ^3 + 11n - 12)2^{n+2} + 6n + 54). Chapter 6 solves a very special degenerate case during the continuation process. The Morse Index of these central configurations is discussed in Chapter 8.

  10. Magnetic flux biasing of magnetostrictive sensors

    NASA Astrophysics Data System (ADS)

    Deng, Zhangxian; Dapino, Marcelo J.

    2017-05-01

    The performance of magnetostrictive materials, especially those with high initial magnetic permeability and associated low magnetic reluctance, is sensitive to not just the amount of magnetic bias but also how the bias is applied. Terfenol-D and Galfenol have been characterized under constant magnetic field and constant magnetomotive force, which require active control. The application of a magnetic flux bias utilizing permanent magnets allows for robust magnetostrictive systems that require no active control. However, this biasing configuration has not been thoroughly investigated. This study presents flux density versus stress major loops of Terfenol-D and Galfenol at various magnetic flux biases. A new piezomagnetic coefficient {d}33φ is defined as the locally-averaged slope of flux density versus stress. Considering the materials alone, the maximum {d}33φ is 18.42 T GPa-1 and 19.53 T GPa-1 for Terfenol-D and Galfenol, respectively. Compared with the peak piezomagnetic coefficient {d}33* measured under controlled magnetic fields, the piezomagnetic coefficient {d}33φ is 26% and 74% smaller for Terfenol-D and Galfenol, respectively. This study shows that adding parallel magnetic flux paths to low-reluctance magnetostrictive components can partially compensate for the performance loss. With a low carbon steel flux path in parallel to the Galfenol specimen, the maximum {d}33φ increased to 28.33 T GPa-1 corresponding to a 45% improvement compared with the case without a flux path. Due to its low magnetic permeability, Terfenol-D does not benefit from the addition of a parallel flux path.

  11. Temperature trend biases

    NASA Astrophysics Data System (ADS)

    Venema, Victor; Lindau, Ralf

    2016-04-01

    In an accompanying talk we show that well-homogenized national dataset warm more than temperatures from global collections averaged over the region of common coverage. In this poster we want to present auxiliary work about possible biases in the raw observations and on how well relative statistical homogenization can remove trend biases. There are several possible causes of cooling biases, which have not been studied much. Siting could be an important factor. Urban stations tend to move away from the centre to better locations. Many stations started inside of urban areas and are nowadays more outside. Even for villages the temperature difference between the centre and edge can be 0.5°C. When a city station moves to an airport, which often happened around WWII, this takes the station (largely) out of the urban heat island. During the 20th century the Stevenson screen was established as the dominant thermometer screen. This screen protected the thermometer much better against radiation than earlier designs. Deficits of earlier measurement methods have artificially warmed the temperatures in the 19th century. Newer studies suggest we may have underestimated the size of this bias. Currently we are in a transition to Automatic Weather Stations. The net global effect of this transition is not clear at this moment. Irrigation on average decreases the 2m-temperature by about 1 degree centigrade. At the same time, irrigation has increased significantly during the last century. People preferentially live in irrigated areas and weather stations serve agriculture. Thus it is possible that there is a higher likelihood that weather stations are erected in irrigated areas than elsewhere. In this case irrigation could lead to a spurious cooling trend. In the Parallel Observations Science Team of the International Surface Temperature Initiative (ISTI-POST) we are studying influence of the introduction of Stevenson screens and Automatic Weather Stations using parallel measurements

  12. Elaborating transition interface sampling methods

    SciTech Connect

    Erp, Titus S. van . E-mail: bolhuis@science.uva.nl

    2005-05-01

    We review two recently developed efficient methods for calculating rate constants of processes dominated by rare events in high-dimensional complex systems. The first is transition interface sampling (TIS), based on the measurement of effective fluxes through hypersurfaces in phase space. TIS improves efficiency with respect to standard transition path sampling (TPS) rate constant techniques, because it allows a variable path length and is less sensitive to recrossings. The second method is the partial path version of TIS. Developed for diffusive processes, it exploits the loss of long time correlation. We discuss the relation between the new techniques and the standard reactive flux methods in detail. Path sampling algorithms can suffer from ergodicity problems, and we introduce several new techniques to alleviate these problems, notably path swapping, stochastic configurational bias Monte Carlo shooting moves and order-parameter free path sampling. In addition, we give algorithms to calculate other interesting properties from path ensembles besides rate constants, such as activation energies and reaction mechanisms.

  13. Elaborating transition interface sampling methods

    NASA Astrophysics Data System (ADS)

    van Erp, Titus S.; Bolhuis, Peter G.

    2005-05-01

    We review two recently developed efficient methods for calculating rate constants of processes dominated by rare events in high-dimensional complex systems. The first is transition interface sampling (TIS), based on the measurement of effective fluxes through hypersurfaces in phase space. TIS improves efficiency with respect to standard transition path sampling (TPS) rate constant techniques, because it allows a variable path length and is less sensitive to recrossings. The second method is the partial path version of TIS. Developed for diffusive processes, it exploits the loss of long time correlation. We discuss the relation between the new techniques and the standard reactive flux methods in detail. Path sampling algorithms can suffer from ergodicity problems, and we introduce several new techniques to alleviate these problems, notably path swapping, stochastic configurational bias Monte Carlo shooting moves and order-parameter free path sampling. In addition, we give algorithms to calculate other interesting properties from path ensembles besides rate constants, such as activation energies and reaction mechanisms.

  14. Recursive bias estimation and L2 boosting

    SciTech Connect

    Hengartner, Nicolas W; Cornillon, Pierre - Andre; Matzner - Lober, Eric

    2009-01-01

    This paper presents a general iterative bias correction procedure for regression smoothers. This bias reduction schema is shown to correspond operationally to the L{sub 2} Boosting algorithm and provides a new statistical interpretation for L{sub 2} Boosting. We analyze the behavior of the Boosting algorithm applied to common smoothers S which we show depend on the spectrum of I - S. We present examples of common smoother for which Boosting generates a divergent sequence. The statistical interpretation suggest combining algorithm with an appropriate stopping rule for the iterative procedure. Finally we illustrate the practical finite sample performances of the iterative smoother via a simulation study.

  15. Sampling designs matching species biology produce accurate and affordable abundance indices

    PubMed Central

    Farley, Sean; Russell, Gareth J.; Butler, Matthew J.; Selinger, Jeff

    2013-01-01

    Wildlife biologists often use grid-based designs to sample animals and generate abundance estimates. Although sampling in grids is theoretically sound, in application, the method can be logistically difficult and expensive when sampling elusive species inhabiting extensive areas. These factors make it challenging to sample animals and meet the statistical assumption of all individuals having an equal probability of capture. Violating this assumption biases results. Does an alternative exist? Perhaps by sampling only where resources attract animals (i.e., targeted sampling), it would provide accurate abundance estimates more efficiently and affordably. However, biases from this approach would also arise if individuals have an unequal probability of capture, especially if some failed to visit the sampling area. Since most biological programs are resource limited, and acquiring abundance data drives many conservation and management applications, it becomes imperative to identify economical and informative sampling designs. Therefore, we evaluated abundance estimates generated from grid and targeted sampling designs using simulations based on geographic positioning system (GPS) data from 42 Alaskan brown bears (Ursus arctos). Migratory salmon drew brown bears from the wider landscape, concentrating them at anadromous streams. This provided a scenario for testing the targeted approach. Grid and targeted sampling varied by trap amount, location (traps placed randomly, systematically or by expert opinion), and traps stationary or moved between capture sessions. We began by identifying when to sample, and if bears had equal probability of capture. We compared abundance estimates against seven criteria: bias, precision, accuracy, effort, plus encounter rates, and probabilities of capture and recapture. One grid (49 km2 cells) and one targeted configuration provided the most accurate results. Both placed traps by expert opinion and moved traps between capture sessions, which

  16. Sampling designs matching species biology produce accurate and affordable abundance indices.

    PubMed

    Harris, Grant; Farley, Sean; Russell, Gareth J; Butler, Matthew J; Selinger, Jeff

    2013-01-01

    Wildlife biologists often use grid-based designs to sample animals and generate abundance estimates. Although sampling in grids is theoretically sound, in application, the method can be logistically difficult and expensive when sampling elusive species inhabiting extensive areas. These factors make it challenging to sample animals and meet the statistical assumption of all individuals having an equal probability of capture. Violating this assumption biases results. Does an alternative exist? Perhaps by sampling only where resources attract animals (i.e., targeted sampling), it would provide accurate abundance estimates more efficiently and affordably. However, biases from this approach would also arise if individuals have an unequal probability of capture, especially if some failed to visit the sampling area. Since most biological programs are resource limited, and acquiring abundance data drives many conservation and management applications, it becomes imperative to identify economical and informative sampling designs. Therefore, we evaluated abundance estimates generated from grid and targeted sampling designs using simulations based on geographic positioning system (GPS) data from 42 Alaskan brown bears (Ursus arctos). Migratory salmon drew brown bears from the wider landscape, concentrating them at anadromous streams. This provided a scenario for testing the targeted approach. Grid and targeted sampling varied by trap amount, location (traps placed randomly, systematically or by expert opinion), and traps stationary or moved between capture sessions. We began by identifying when to sample, and if bears had equal probability of capture. We compared abundance estimates against seven criteria: bias, precision, accuracy, effort, plus encounter rates, and probabilities of capture and recapture. One grid (49 km(2) cells) and one targeted configuration provided the most accurate results. Both placed traps by expert opinion and moved traps between capture sessions

  17. Nonlinear vs. linear biasing in Trp-cage folding simulations

    SciTech Connect

    Spiwok, Vojtěch Oborský, Pavel; Králová, Blanka; Pazúriková, Jana

    2015-03-21

    Biased simulations have great potential for the study of slow processes, including protein folding. Atomic motions in molecules are nonlinear, which suggests that simulations with enhanced sampling of collective motions traced by nonlinear dimensionality reduction methods may perform better than linear ones. In this study, we compare an unbiased folding simulation of the Trp-cage miniprotein with metadynamics simulations using both linear (principle component analysis) and nonlinear (Isomap) low dimensional embeddings as collective variables. Folding of the mini-protein was successfully simulated in 200 ns simulation with linear biasing and non-linear motion biasing. The folded state was correctly predicted as the free energy minimum in both simulations. We found that the advantage of linear motion biasing is that it can sample a larger conformational space, whereas the advantage of nonlinear motion biasing lies in slightly better resolution of the resulting free energy surface. In terms of sampling efficiency, both methods are comparable.

  18. Carrier-type-dependent thermoelectric response of the superconductor-normal-metal-superconductor configuration in a C-shaped polycrystalline BixPb1-xSr2CaCu2Oy sample

    NASA Astrophysics Data System (ADS)

    Gridin, Vladimir V.; Sergeenkov, Sergei A.; Doyle, Richard A.; de Villiers, Patrick; Ausloos, Marcel

    1993-06-01

    Two cuts were inserted at 90° to each other into a ring-shaped sample of BixPb1-xSr2CaCu2Oy. The first cut lay parallel to the applied temperature gradient serving to define a vertical symmetry axis. The second cut lay in the middle of the right wing, perpendicular to the symmetry axis, completely interrupting the passage of supercurrents in this wing. The passage of any normal component of current density was made possible, however, by filling up the cut with a metal that does not show any superconducting properties in the vicinity of 110 K. The carrier type of this normal-metal insert was alternatively chosen to be predominantly holelike (an In insert) or electronlike (Ag paste supporting a 70-Å-thick Au strip). The left wing was left as sintered. Thermal voltages resulting from the same temperature gradient acting on both continuous and normal-metal-filled halves of the sample were detected as a function of temperature around the superconducting transition at about 109 K. Comparing the difference between the thermopowers of the two halves, ΔS, we calculate the Fermi energy of our superconducting material. ΔS was found to be positive and negative for the h- and e-type carriers of the normal-metal insert, respectively. Relating ΔS to the transport entropy, Δσ, via the carrier charge, q, by ΔS=Δσ/q, we also account for the carrier-sign dependence of ΔS.

  19. Configurational asymmetry in vernier offset detection.

    PubMed

    Karim, A K M Rezaul; Kojima, Haruyuki

    2010-10-06

    Two psychophysical experiments were conducted at the horizontal and vertical orientations respectively, demonstrating substantial main effect of configuration, but no effect of offset direction on vernier acuity. In Experiment 1, a pair of horizontal bars were arranged side by side with a large gap between them. The observers were, on average, significantly better at discriminating a vertical offset if the right-hand bar was below the left-hand bar than vice versa, regardless of which bar they experienced as displaced and which as constant. A similar asymmetry was evident in Experiment 2 where observers judged horizontal offset for a pair of vertically oriented bars, where one was placed above the other. In this case average performance was better if the upper bar was on the right of the lower bar rather than on its left. There were large individual variations in the asymmetrical trend, but the effect could not be explained by subjective response bias. Furthermore, vernier acuity improved significantly and the asymmetry decreased more or less as a function of training. The average asymmetrical trend was consistent across training days and across two orientations, which indicates that the processing of line vernier stimuli is possibly configuration-specific in the cardinal orientation.

  20. Configurational asymmetry in vernier offset detection

    PubMed Central

    Karim, A. K. M. Rezaul; Kojima, Haruyuki

    2010-01-01

    Two psychophysical experiments were conducted at the horizontal and vertical orientations respectively, demonstrating substantial main effect of configuration, but no effect of offset direction on vernier acuity. In Experiment 1, a pair of horizontal bars were arranged side by side with a large gap between them. The observers were, on average, significantly better at discriminating a vertical offset if the right-hand bar was below the left-hand bar than vice versa, regardless of which bar they experienced as displaced and which as constant. A similar asymmetry was evident in Experiment 2 where observers judged horizontal offset for a pair of vertically oriented bars, where one was placed above the other. In this case average performance was better if the upper bar was on the right of the lower bar rather than on its left. There were large individual variations in the asymmetrical trend, but the effect could not be explained by subjective response bias. Furthermore, vernier acuity improved significantly and the asymmetry decreased more or less as a function of training. The average asymmetrical trend was consistent across training days and across two orientations, which indicates that the processing of line vernier stimuli is possibly configuration-specific in the cardinal orientation. PMID:20930953

  1. Terrestrial Laser Scanning for Vegetation Sampling

    PubMed Central

    Richardson, Jeffrey J; Moskal, L. Monika; Bakker, Jonathan D.

    2014-01-01

    We developed new vegetation indices utilizing terrestrial laser scanning (TLS) to quantify the three-dimensional spatial configuration of plant communities. These indices leverage the novelty of TLS data and rely on the spatially biased arrangement of a TLS point cloud. We calculated these indices from TLS data acquired within an existing long term manipulation of forest structure in Central Oregon, USA, and used these data to test for differences in vegetation structure. Results provided quantitative evidence of a significant difference in vegetation density due to thinning and burning, and a marginally significant difference in vegetation patchiness due to grazing. A comparison to traditional field sampling highlighted the novelty of the TLS based method. By creating a linkage between traditional field sampling and landscape ecology, these indices enable field investigations of fine-scale spatial patterns. Applications include experimental assessment, long-term monitoring, and habitat characterization. PMID:25353981

  2. Central configurations for -body problems

    NASA Astrophysics Data System (ADS)

    Zhao, Furong; Chen, Jian

    2015-01-01

    We show the existence of planar central configurations for -body problems with Newtonian potentials; in such configurations, -bodies are located at the vertices of regular -gons with a common center, where regular -gons are homothetic, and regular -gons are homothetic rotated by compared to the first set of -gons, and all masses on the same -gon are equal.

  3. Configurational entropy of glueball states

    NASA Astrophysics Data System (ADS)

    Bernardini, Alex E.; Braga, Nelson R. F.; da Rocha, Roldão

    2017-02-01

    The configurational entropy of glueball states is calculated using a holographic description. Glueball states are represented by a supergravity dual picture, consisting of a 5-dimensional graviton-dilaton action of a dynamical holographic AdS/QCD model. The configurational entropy is studied as a function of the glueball spin and of the mass, providing information about the stability of the glueball states.

  4. Configuration of Appalachian logging roads

    Treesearch

    John E. Baumgras; John E. Baumgras

    1971-01-01

    The configuration - the curvature and grade - of logging roads in southern Appalachia is seldom severe, according to a recent Forest Service study. To improve the efficiency of logging roads, we must first define the characteristics of these roads; and in this report we provide a quantitative description of the configuration of over 200 miles of logging roads.

  5. Investigating the Stability of Four Methods for Estimating Item Bias.

    ERIC Educational Resources Information Center

    Perlman, Carole L.; And Others

    The reliability of item bias estimates was studied for four methods: (1) the transformed delta method; (2) Shepard's modified delta method; (3) Rasch's one-parameter residual analysis; and (4) the Mantel-Haenszel procedure. Bias statistics were computed for each sample using all methods. Data were from administration of multiple-choice items from…

  6. Why is "S" a Biased Estimate of [sigma]?

    ERIC Educational Resources Information Center

    Sanqui, Jose Almer T.; Arnholt, Alan T.

    2011-01-01

    This article describes a simulation activity that can be used to help students see that the estimator "S" is a biased estimator of [sigma]. The activity can be implemented using either a statistical package such as R, Minitab, or a Web applet. In the activity, the students investigate and compare the bias of "S" when sampling from different…

  7. LETTER TO THE EDITOR: Bias analysis in entropy estimation

    NASA Astrophysics Data System (ADS)

    Schürmann, Thomas

    2004-07-01

    We consider the problem of finite sample corrections for entropy estimation. New estimates of the Shannon entropy are proposed and their systematic error (the bias) is computed analytically. We find that our results cover correction formulae of current entropy estimates recently discussed in the literature. The trade-off between bias reduction and the increase of the corresponding statistical error is analysed.

  8. Why is "S" a Biased Estimate of [sigma]?