Science.gov

Sample records for configuration bias sampling

  1. A new configurational bias scheme for sampling supramolecular structures

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    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. 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.

  3. A new configurational bias scheme for sampling supramolecular structures.

    PubMed

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

    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. PMID:25554182

  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. PMID:25770522

  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 biases in CMIP5 decadal forecasts

    NASA Astrophysics Data System (ADS)

    Choudhury, Dipayan; Sharma, Ashish; Sen Gupta, Alexander; Mehrotra, Rajeshwar; Sivakumar, Bellie

    2016-04-01

    Recent studies examining the fidelity of decadal hindcast experiments from phase 5 of the Coupled Model Intercomparison Project have highlighted the need for larger ensembles of forecasts, compared to the initial five yearly spaced initializations, to help correct for model biases (drift). This study quantifies differences in the two drift estimates in sea surface temperature (SST) and SST anomaly (SSTA) predictions, between experiments initialized every 5 years and those initialized every year. The effect of the recommended mean drift correction, on the two sets of predictions, is also analyzed. Our results indicate that differences between the SST drift estimates are largest over the tropical Pacific. Moreover, this difference is large for Niño 3.4 and almost negligible for the global average SSTA. Drift correction as per the mean drift from the 5 year case leads to spurious peaks in the drift-corrected Niño 3.4 (and the tropical Pacific) and sporadic improvements in skill. This problem with Niño 3.4 stems from an aliasing that occurs during the drift calculation that results from a combination of the timing of major El Niño events in relation to the initialization dates. The study recommends accounting for such sampling effects while considering any subset of the full data set.

  8. Rational Learning and Information Sampling: On the "Naivety" Assumption in Sampling Explanations of Judgment Biases

    ERIC Educational Resources Information Center

    Le Mens, Gael; Denrell, Jerker

    2011-01-01

    Recent research has argued that several well-known judgment biases may be due to biases in the available information sample rather than to biased information processing. Most of these sample-based explanations assume that decision makers are "naive": They are not aware of the biases in the available information sample and do not correct for them.…

  9. 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.

  10. Improvement in bias current redistribution in superconducting strip ion detectors with parallel configuration

    NASA Astrophysics Data System (ADS)

    Nobuyuki, Zen; Go, Fujii; Shigetomo, Shiki; Masahiro, Ukibe; Masaki, Koike; Masataka, Ohkubo

    2015-09-01

    In time-of-flight mass spectrometry (TOF MS), superconducting strip ion detectors (SSIDs) in the parallel configuration are promising for ideal ion detection with a nanosecond-scale time response and a practical large sensitive area. In the parallel configuration, the bias current in one strip is diverted into other parallel strips after each detection event. Under high bias current conditions, the diverted bias current induces cascade switching of all parallel strips. Studies show that cascade switching degrades the ion count rate of SSIDs made from niobium and hence is disliked in TOF MS applications. To suppress the bias current redistribution, we connected resistors in a series with the individual parallel strips using aluminum-bonding wires. Their effect was studied by measuring the pulse height distributions. Project supported by a Grant-in-Aid for Scientific Research (A) and (C) from the Japan Society for the Promotion of Science (Grant Nos. 22246056 and 24619013).

  11. Radial profile of plasma potential with various biased electrode ring configurations in a toroidal plasma

    SciTech Connect

    Chaube, N.R.; Jain, K.K.

    1996-07-01

    An experimental study on behavior of radial profile of the floating potential with different biased electrode ring configurations has been carried out in a currentless magnetized toroidal plasma. Radial profile of the floating potential has been measured by biasing single ring of various sizes and two rings. It is observed that floating potential profile of a well shaped with controllable depth, hill-cum-well shaped, and almost flat positive potential can be obtained. Results on parameter dependence studies of floating potential on the bias voltage, magnetic field, and gas pressure are presented. {copyright} {ital 1996 American Institute of Physics.}

  12. 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. PMID:26941240

  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. 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...

  15. 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...

  16. 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

  17. 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. PMID:26679927

  18. The World of Hidden Biases: From Collection to Sample Processing

    NASA Astrophysics Data System (ADS)

    Maurette, Michel

    Any study of micrometeorites involves a variety of biases, which start right away during their collection, and which have not been suffciently publicized. This section deals with the astonishing folklore of these biases. We shall question whether major differences observed between Antarctic micrometeorites and stratospheric micrometeorites could reflect kinds of complementary biases between the two collections of micrometeorites. Astonishingly, some of them would converge to enrich the SMMs collection in the most fine-grained fluffy dust particles accreted by the Earth. They might be possibly the most primitive material accreted by the Earth. But they would not give a representative sampling of the bulk micrometeorite flux, which is best obtained with the new Concordia micrometeorites collected in central Antarctica. For a change, biases developing around a small metallic plate flying at ~200m/sec in the stratosphere turned out to be quite helpful!

  19. 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,…

  20. 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

  1. 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

  2. Reducing sample variance: halo biasing, non-linearity and stochasticity

    NASA Astrophysics Data System (ADS)

    Gil-Marín, Héctor; Wagner, Christian; Verde, Licia; Jimenez, Raul; Heavens, Alan F.

    2010-09-01

    Comparing clustering of differently biased tracers of the dark matter distribution offers the opportunity to reduce the sample or cosmic variance error in the measurement of certain cosmological parameters. We develop a formalism that includes bias non-linearities and stochasticity. Our formalism is general enough that it can be used to optimize survey design and tracers selection and optimally split (or combine) tracers to minimize the error on the cosmologically interesting quantities. Our approach generalizes the one presented by McDonald & Seljak of circumventing sample variance in the measurement of f ≡ d lnD/d lna. We analyse how the bias, the noise, the non-linearity and stochasticity affect the measurements of Df and explore in which signal-to-noise regime it is significantly advantageous to split a galaxy sample in two differently biased tracers. We use N-body simulations to find realistic values for the parameters describing the bias properties of dark matter haloes of different masses and their number density. We find that, even if dark matter haloes could be used as tracers and selected in an idealized way, for realistic haloes, the sample variance limit can be reduced only by up to a factor σ2tr/σ1tr ~= 0.6. This would still correspond to the gain from a three times larger survey volume if the two tracers were not to be split. Before any practical application one should bear in mind that these findings apply to dark matter haloes as tracers, while realistic surveys would select galaxies: the galaxy-host halo relation is likely to introduce extra stochasticity, which may reduce the gain further.

  3. 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

  4. Species richness in the Phanerozoic: Compensating for sampling bias

    NASA Astrophysics Data System (ADS)

    Signor, Philip W., III

    1982-12-01

    Sampling biases are the greatest impediment to resolving the history of species richness of fossilizable marine invertebrates in the Phanerozoic. Actual patterns of species richness have remained uncertain because no method is available to compensate for variations in sampling intensity. Data are not obtainable which would permit application of techniques that allow direct compensation for sampling intensity, such as rarefaction, but actual patterns can be estimated with a sampling model designed to account for sampling bias. One can estimate the total species richness of a geologic period if one knows the relative sampling intensity devoted to that period, the original species-abundance distribution of all species that existed during the interval, and the number of species that existed during the Cenozoic. The model presented here is based on the assumption that the species-abundance distributions of fossilizable marine invertebrates were lognormal and that sampling was proportional to sediment area, volume, or paleontologist interest units. The model produces consistent results with different estimates of total Cenozoic species richness and sampling intensity and strongly suggests low diversity during the Paleozoic and Mesozoic, followed by a dramatic early Cenozoic increase in standing species richness. These results are consistent with Valentine's (1970) Empirical model of species richness.

  5. Field Reversed Configuration Confinement Enhancement through Edge Biasing and Neutral Beam Injection

    NASA Astrophysics Data System (ADS)

    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.

    2012-06-01

    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.

  6. 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. PMID:23004613

  7. 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

    2012-01-01

    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. PMID:23092978

  8. Sample Collection Method Bias Effects in Quantitative Phosphoproteomics.

    PubMed

    Kanshin, Evgeny; Tyers, Michael; Thibault, Pierre

    2015-07-01

    Current advances in selective enrichment, fractionation, and MS detection of phosphorylated peptides allowed identification and quantitation of tens of thousands phosphosites from minute amounts of biological material. One of the major challenges in the field is preserving the in vivo phosphorylation state of the proteins throughout the sample preparation workflow. This is typically achieved by using phosphatase inhibitors and denaturing conditions during cell lysis. Here we determine if the upstream cell collection techniques could introduce changes in protein phosphorylation. To evaluate the effect of sample collection protocols on the global phosphorylation status of the cell, we compared different sample workflows by metabolic labeling and quantitative mass spectrometry on Saccharomyces cerevisiae cell cultures. We identified highly similar phosphopeptides for cells harvested in ice cold isotonic phosphate buffer, cold ethanol, trichloroacetic acid, and liquid nitrogen. However, quantitative analyses revealed that the commonly used phosphate buffer unexpectedly activated signaling events. Such effects may introduce systematic bias in phosphoproteomics measurements and biochemical analysis. PMID:26040406

  9. 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. PMID:21290401

  10. Configurational bias Monte Carlo simulation of phase segregation in block copolymer networks.

    PubMed

    Palmer, Kent I; Lastoskie, Christian M

    2004-01-01

    Cross-linked block copolymers are used as adhesives in fiber-reinforced composite material manufactures for automotive applications. Good adhesion between the polymer matrix and fibers in the interphase region is required for the structural integrity of these materials. Experimental evidence indicates that superior adhesion is obtained when phase segregation occurs between the two matrix phase block copolymers. It is therefore desirable to predict the conditions under which phase segregation is expected to occur. Configurational bias Monte Carlo simulations of two-component, trifunctional block copolymer networks were carried out to investigate phase segregation in these materials. The effects of four principal parameters on phase segregation were examined: the weight fractions of the two components, the cross-link length, the connectivity of the network, and the ratio of the square-well interactions. The molecular simulation results confirmed trends observed in laboratory measurements. PMID:15267310

  11. 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

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

    PubMed

    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

  13. Cognition and Instruction: Reasoning about bias in sampling

    NASA Astrophysics Data System (ADS)

    Watson, Jane; Kelly, Ben

    2005-02-01

    Although sampling has been mentioned as part of the chance and data component of the mathematics curriculum since about 1990, little research attention has been aimed specifically at school students' understanding of this descriptive area. This study considers the initial understanding of bias in sampling by 639 students in grades 3, 5, 7, and 9. Three hundred and forty-one of these students then undertook a series of lessons on chance and data with an emphasis on chance, data handling, sampling, and variation. A post-test was administered to 285 of these students and two years later all available students from the original group (328) were again tested. This study considers the initial level of understanding of students, the nature of the lessons undertaken at each grade level, the post-instruction performance of those who undertook lessons, and the longitudinal performance after two years of all available students. Overall instruction was associated with improved performance, which was retained over two years but there was little difference between those who had or had not experienced instruction. Results for specific grades, some of which went against the overall trend are discussed, as well as educational implications for the teaching of sampling across the years of schooling based on the classroom observations and the changes observed.

  14. Social sampling explains apparent biases in judgments of social environments.

    PubMed

    Galesic, Mirta; Olsson, Henrik; Rieskamp, Jörg

    2012-12-01

    How people assess their social environments plays a central role in how they evaluate their life circumstances. Using a large probabilistic national sample, we investigated how accurately people estimate characteristics of the general population. For most characteristics, people seemed to underestimate the quality of others' lives and showed apparent self-enhancement, but for some characteristics, they seemed to overestimate the quality of others' lives and showed apparent self-depreciation. In addition, people who were worse off appeared to enhance their social position more than those who were better off. We demonstrated that these effects can be explained by a simple social-sampling model. According to the model, people infer how others are doing by sampling from their own immediate social environments. Interplay of these sampling processes and the specific structure of social environments leads to the apparent biases. The model predicts the empirical results better than alternative accounts and highlights the importance of considering environmental structure when studying human cognition. PMID:23104680

  15. 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

  16. Using self-consistent fields to bias Monte Carlo methods with applications to designing and sampling protein sequences

    NASA Astrophysics Data System (ADS)

    Zou, Jinming; Saven, Jeffery G.

    2003-02-01

    For complex multidimensional systems, Monte Carlo methods are useful for sampling probable regions of a configuration space and, in the context of annealing, for determining "low energy" or "high scoring" configurations. Such methods have been used in protein design as means to identify amino acid sequences that are energetically compatible with a particular backbone structure. As with many other applications of Monte Carlo methods, such searches can be inefficient if trial configurations (protein sequences) in the Markov chain are chosen randomly. Here a mean-field biased Monte Carlo method (MFBMC) is presented and applied to designing and sampling protein sequences. The MFBMC method uses predetermined sequence identity probabilities wi(α) to bias the sequence selection. The wi(α) are calculated using a self-consistent, mean-field theory that can estimate the number and composition of sequences having predetermined values of energetically related foldability criteria. The MFBMC method is applied to both a simple protein model, the 27-mer lattice model, and an all-atom protein model. Compared to conventional Monte Carlo (MC) and configurational bias Monte Carlo (BMC), the MFBMC method converges faster to low energy sequences and samples such sequences more efficiently. The MFBMC method also tolerates faster cooling rates than the MC and BMC methods. The MFBMC method can be applied not only to protein sequence search, but also to a wide variety of polymeric and condensed phase systems.

  17. 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.

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

    PubMed

    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. We 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. PMID:6720582

  19. Characterizing sampling biases in the trace gas climatologies of the SPARC Data Initiative

    NASA Astrophysics Data System (ADS)

    Toohey, M.; Hegglin, M. I.; Tegtmeier, S.; Anderson, J.; Añel, J. A.; Bourassa, A.; Brohede, S.; Degenstein, D.; Froidevaux, L.; Fuller, R.; Funke, B.; Gille, J.; Jones, A.; Kasai, Y.; Krüger, K.; Kyrölä, E.; Neu, J. L.; Rozanov, A.; Smith, L.; Urban, J.; Clarmann, T.; Walker, K. A.; Wang, R. H. J.

    2013-10-01

    zonal mean climatologies of atmospheric measurements from satellite instruments can have biases due to the nonuniform sampling of the atmosphere by the instruments. We characterize potential sampling biases in stratospheric trace gas climatologies of the Stratospheric Processes and Their Role in Climate (SPARC) Data Initiative using chemical fields from a chemistry climate model simulation and sampling patterns from 16 satellite-borne instruments. The exercise is performed for the long-lived stratospheric trace gases O3 and H2O. Monthly sampling biases for O3 exceed 10% for many instruments in the high-latitude stratosphere and in the upper troposphere/lower stratosphere, while annual mean sampling biases reach values of up to 20% in the same regions for some instruments. Sampling biases for H2O are generally smaller than for O3, although still notable in the upper troposphere/lower stratosphere and Southern Hemisphere high latitudes. The most important mechanism leading to monthly sampling bias is nonuniform temporal sampling, i.e., the fact that for many instruments, monthly means are produced from measurements which span less than the full month in question. Similarly, annual mean sampling biases are well explained by nonuniformity in the month-to-month sampling by different instruments. Nonuniform sampling in latitude and longitude are shown to also lead to nonnegligible sampling biases, which are most relevant for climatologies which are otherwise free of biases due to nonuniform temporal sampling.

  20. The association between negative attention biases and symptoms of depression in a community sample of adolescents

    PubMed Central

    Murphy, Susannah E.; Lau, Jennifer Y.F.

    2015-01-01

    Adolescence is a vulnerable time for the onset of depression. Recent evidence from adult studies suggests not only that negative attention biases are correlated with symptoms of depression, but that reducing negative attention biases through training can in turn reduce symptomology. The role and plasticity of attention biases in adolescent depression, however, remains unclear. This study examines the association between symptoms of depression and attention biases, and whether such biases are modifiable, in a community sample of adolescents. We report data from 105 adolescents aged 13–17 who completed a dot-probe measure of attention bias before and after a single session of visual search-based cognitive bias modification training. This is the first study to find a significant association between negative attention biases and increased symptoms of depression in a community sample of adolescents. Contrary to expectations, we were unable to manipulate attention biases using a previously successful cognitive bias modification task. There were no significant effects of the training on positive affect and only modest effects of the training, identified in post-hoc analyses, were observed on negative affect. Our data replicate those from the adult literature, which suggest that adolescent depression is a disorder associated with negative attention biases, although we were unable to modify attention biases in our study. We identify numerous parameters of our methodology which may explain these null training effects, and which could be addressed in future cognitive bias modification studies of adolescent depression. PMID:26539335

  1. 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…

  2. 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.

  3. 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…

  4. Fraction of Clogging Configurations Sampled by Granular Hopper Flow

    NASA Astrophysics Data System (ADS)

    Thomas, C. C.; Durian, D. J.

    2015-05-01

    We measure the fraction F of flowing grain configurations that precede a clog, based on the average mass discharged between clogging events for various aperture geometries. By tilting the hopper, we demonstrate that F is a function of the hole area projected in the direction of the exiting grain velocity. By varying the length of slits, we demonstrate that grains clog in the same manner as if they were flowing out of a set of smaller independent circular openings. The collapsed data for F can be fit to a decay that is exponential in hole width raised to the power of the system dimensionality. This is consistent with a simple model in which individual grains near the hole have a large but constant probability to precede a clog. Such a picture implies that there is no sharp clogging transition, and that all hoppers have a nonzero probability to clog.

  5. Density-Biased Sampling: A Robust Computational Method for Studying Pore Formation in Membranes

    PubMed Central

    2015-01-01

    A new reaction coordinate to bias molecular dynamics simulation is described that allows enhanced sampling of density-driven processes, such as mixing and demixing two different molecular species. The methodology is validated by comparing the theoretical entropy of demixing two ideal gas species and then applied to induce deformation and pore formation in phospholipid membranes within an umbrella sampling framework. Comparison with previous biased simulations of membrane pore formation suggests overall quantitative agreement, but the density-based biasing potential results in a different, more realistic transition pathway than that in previous studies. PMID:25620896

  6. 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.

  7. 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

  8. 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. PMID:27496360

  9. 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.

  10. Biomass and abundance biases in European standard gillnet sampling.

    PubMed

    Šmejkal, Marek; Ricard, Daniel; Prchalová, Marie; Říha, Milan; Muška, Milan; Blabolil, Petr; Čech, Martin; Vašek, Mojmír; Jůza, Tomáš; Monteoliva Herreras, Agustín; Encina, Lourdes; Peterka, Jiří; Kubečka, Jan

    2015-01-01

    The European Standard EN 14757 recommends gillnet mesh sizes that range from 5 to 55mm (knot-to-knot) for the standard monitoring of fish assemblages and suggests adding gillnets with larger mesh sizes if necessary. Our research showed that the recommended range of mesh sizes did not provide a representative picture of fish sizes for larger species that commonly occur in continental Europe. We developed a novel, large mesh gillnet which consists of mesh sizes 70, 90, 110 and 135mm (knot to knot, 10m panels) and assessed its added value for monitoring purposes. From selectivity curves obtained by sampling with single mesh size gillnets (11 mesh sizes 6 - 55mm) and large mesh gillnets, we identified the threshold length of bream (Abramis brama) above which this widespread large species was underestimated by European standard gillnet catches. We tested the European Standard gillnet by comparing its size composition with that obtained during concurrent pelagic trawling and purse seining in a cyprinid-dominated reservoir and found that the European Standard underestimated fish larger than 292mm by 26 times. The inclusion of large mesh gillnets in the sampling design removed this underestimation. We analysed the length-age relationship of bream in the Římov Reservoir, and concluded that catches of bream larger than 292mm and older than five years were seriously underrepresented in European Standard gillnet catches. The Římov Reservoir is a typical cyprinid-dominated water body where the biomass of bream > 292mm formed 70% of the pelagic trawl and purse seine catch. The species-specific relationships between the large mesh gillnet catch and European Standard catch suggested that the presence of carp (Cyprinus carpio), European catfish (Silurus glanis), tench (Tinca tinca) or bream warrants the use of both gillnet types. We suggest extending the gillnet series in the European Standard to avoid misinterpretation of fish community biomass estimates. PMID:25793776

  11. Biomass and Abundance Biases in European Standard Gillnet Sampling

    PubMed Central

    Prchalová, Marie; Říha, Milan; Muška, Milan; Blabolil, Petr; Čech, Martin; Vašek, Mojmír; Jůza, Tomáš; Monteoliva Herreras, Agustín; Encina, Lourdes; Peterka, Jiří; Kubečka, Jan

    2015-01-01

    The European Standard EN 14757 recommends gillnet mesh sizes that range from 5 to 55mm (knot-to-knot) for the standard monitoring of fish assemblages and suggests adding gillnets with larger mesh sizes if necessary. Our research showed that the recommended range of mesh sizes did not provide a representative picture of fish sizes for larger species that commonly occur in continental Europe. We developed a novel, large mesh gillnet which consists of mesh sizes 70, 90, 110 and 135mm (knot to knot, 10m panels) and assessed its added value for monitoring purposes. From selectivity curves obtained by sampling with single mesh size gillnets (11 mesh sizes 6 – 55mm) and large mesh gillnets, we identified the threshold length of bream (Abramis brama) above which this widespread large species was underestimated by European standard gillnet catches. We tested the European Standard gillnet by comparing its size composition with that obtained during concurrent pelagic trawling and purse seining in a cyprinid-dominated reservoir and found that the European Standard underestimated fish larger than 292mm by 26 times. The inclusion of large mesh gillnets in the sampling design removed this underestimation. We analysed the length-age relationship of bream in the Římov Reservoir, and concluded that catches of bream larger than 292mm and older than five years were seriously underrepresented in European Standard gillnet catches. The Římov Reservoir is a typical cyprinid-dominated water body where the biomass of bream > 292mm formed 70% of the pelagic trawl and purse seine catch. The species-specific relationships between the large mesh gillnet catch and European Standard catch suggested that the presence of carp (Cyprinus carpio), European catfish (Silurus glanis), tench (Tinca tinca) or bream warrants the use of both gillnet types. We suggest extending the gillnet series in the European Standard to avoid misinterpretation of fish community biomass estimates. PMID:25793776

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    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 × 1011 Am-2.

  13. 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.

  14. Effects of Sample Selection Bias on the Accuracy of Population Structure and Ancestry Inference

    PubMed Central

    Shringarpure, Suyash; Xing, Eric P.

    2014-01-01

    Population stratification is an important task in genetic analyses. It provides information about the ancestry of individuals and can be an important confounder in genome-wide association studies. Public genotyping projects have made a large number of datasets available for study. However, practical constraints dictate that of a geographical/ethnic population, only a small number of individuals are genotyped. The resulting data are a sample from the entire population. If the distribution of sample sizes is not representative of the populations being sampled, the accuracy of population stratification analyses of the data could be affected. We attempt to understand the effect of biased sampling on the accuracy of population structure analysis and individual ancestry recovery. We examined two commonly used methods for analyses of such datasets, ADMIXTURE and EIGENSOFT, and found that the accuracy of recovery of population structure is affected to a large extent by the sample used for analysis and how representative it is of the underlying populations. Using simulated data and real genotype data from cattle, we show that sample selection bias can affect the results of population structure analyses. We develop a mathematical framework for sample selection bias in models for population structure and also proposed a correction for sample selection bias using auxiliary information about the sample. We demonstrate that such a correction is effective in practice using simulated and real data. PMID:24637351

  15. Specific and Non-Specific Protein Association in Solution: Computation of Solvent Effects and Prediction of First-Encounter Modes for Efficient Configurational Bias Monte Carlo Simulations

    PubMed Central

    Cardone, Antonio; Pant, Harish; Hassan, Sergio A.

    2013-01-01

    Weak and ultra-weak protein-protein association play a role in molecular recognition, and can drive spontaneous self-assembly and aggregation. Such interactions are difficult to detect experimentally, and are a challenge to the force field and sampling technique. A method is proposed to identify low-population protein-protein binding modes in aqueous solution. The method is designed to identify preferential first-encounter complexes from which the final complex(es) at equilibrium evolves. A continuum model is used to represent the effects of the solvent, which accounts for short- and long-range effects of water exclusion and for liquid-structure forces at protein/liquid interfaces. These effects control the behavior of proteins in close proximity and are optimized based on binding enthalpy data and simulations. An algorithm is described to construct a biasing function for self-adaptive configurational-bias Monte Carlo of a set of interacting proteins. The function allows mixing large and local changes in the spatial distribution of proteins, thereby enhancing sampling of relevant microstates. The method is applied to three binary systems. Generalization to multiprotein complexes is discussed. PMID:24044772

  16. Validation sampling can reduce bias in healthcare database studies: an illustration using influenza vaccination effectiveness

    PubMed Central

    Nelson, Jennifer C.; Marsh, Tracey; Lumley, Thomas; Larson, Eric B.; Jackson, Lisa A.; Jackson, Michael

    2014-01-01

    Objective Estimates of treatment effectiveness in epidemiologic studies using large observational health care databases may be biased due to inaccurate or incomplete information on important confounders. Study methods that collect and incorporate more comprehensive confounder data on a validation cohort may reduce confounding bias. Study Design and Setting We applied two such methods, imputation and reweighting, to Group Health administrative data (full sample) supplemented by more detailed confounder data from the Adult Changes in Thought study (validation sample). We used influenza vaccination effectiveness (with an unexposed comparator group) as an example and evaluated each method’s ability to reduce bias using the control time period prior to influenza circulation. Results Both methods reduced, but did not completely eliminate, the bias compared with traditional effectiveness estimates that do not utilize the validation sample confounders. Conclusion Although these results support the use of validation sampling methods to improve the accuracy of comparative effectiveness findings from healthcare database studies, they also illustrate that the success of such methods depends on many factors, including the ability to measure important confounders in a representative and large enough validation sample, the comparability of the full sample and validation sample, and the accuracy with which data can be imputed or reweighted using the additional validation sample information. PMID:23849144

  17. Bespoke Bias for Obtaining Free Energy Differences within Variationally Enhanced Sampling.

    PubMed

    McCarty, James; Valsson, Omar; Parrinello, Michele

    2016-05-10

    Obtaining efficient sampling of multiple metastable states through molecular dynamics and hence determining free energy differences is central for understanding many important phenomena. Here we present a new biasing strategy, which employs the recent variationally enhanced sampling approach (Valsson and Parrinello Phys. Rev. Lett. 2014, 113, 090601). The bias is constructed from an intuitive model of the local free energy surface describing fluctuations around metastable minima and depends on only a few parameters which are determined variationally such that efficient sampling between states is obtained. The bias constructed in this manner largely reduces the need of finding a set of collective variables that completely spans the conformational space of interest, as they only need to be a locally valid descriptor of the system about its local minimum. We introduce the method and demonstrate its power on two representative examples. PMID:27057791

  18. 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

  19. Heat-Bath Configuration Interaction: An Efficient Selected Configuration Interaction Algorithm Inspired by Heat-Bath Sampling.

    PubMed

    Holmes, Adam A; Tubman, Norm M; Umrigar, C J

    2016-08-01

    We introduce a new selected configuration interaction plus perturbation theory algorithm that is based on a deterministic analog of our recent efficient heat-bath sampling algorithm. This Heat-bath Configuration Interaction (HCI) algorithm makes use of two parameters that control the trade-off between speed and accuracy, one which controls the selection of determinants to add to a variational wave function and one which controls the selection of determinants used to compute the perturbative correction to the variational energy. We show that HCI provides an accurate treatment of both static and dynamic correlation by computing the potential energy curve of the multireference carbon dimer in the cc-pVDZ basis. We then demonstrate the speed and accuracy of HCI by recovering the full configuration interaction energy of both the carbon dimer in the cc-pVTZ basis and the strongly correlated chromium dimer in the Ahlrichs VDZ basis, correlating all electrons, to an accuracy of better than 1 mHa, in just a few minutes on a single core. These systems have full variational spaces of 3 × 10(14) and 2 × 10(22) determinants, respectively. PMID:27428771

  20. Evaluation of the Validity of Crystallization Temperature Measurements Using Thermography with Different Sample Configurations

    NASA Astrophysics Data System (ADS)

    Yuko Aono,; Junpei Sakurai,; Akira Shimokohbe,; Seiichi Hata,

    2010-07-01

    We describe further progress of a previously reported novel crystallization temperature (Tx) measurement method applicable for small sample sizes. The method uses thermography and detects Tx as a change in emissivity of thin film amorphous alloy samples. We applied this method to various sample configurations of Pd-Cu-Si thin film metallic glass (TFMG). The validity of the detected Tx was determined by electrical resistivity monitoring and differential scanning calorimetry (DSC). Crystallization temperature can be detected in all sample configurations; however, it was found that the magnitude of the detected change of emissivity at Tx depended on the sample configuration. This emissivity change was clear in the absence of a higher emissivity material. The results suggest that this method can achieve high-throughput characterization of Tx for integrated small samples such as in a thin film library.

  1. Bias of shear wave elasticity measurements in thin layer samples and a simple correction strategy.

    PubMed

    Mo, Jianqiang; Xu, Hao; Qiang, Bo; Giambini, Hugo; Kinnick, Randall; An, Kai-Nan; Chen, Shigao; Luo, Zongping

    2016-01-01

    Shear wave elastography (SWE) is an emerging technique for measuring biological tissue stiffness. However, the application of SWE in thin layer tissues is limited by bias due to the influence of geometry on measured shear wave speed. In this study, we investigated the bias of Young's modulus measured by SWE in thin layer gelatin-agar phantoms, and compared the result with finite element method and Lamb wave model simulation. The result indicated that the Young's modulus measured by SWE decreased continuously when the sample thickness decreased, and this effect was more significant for smaller thickness. We proposed a new empirical formula which can conveniently correct the bias without the need of using complicated mathematical modeling. In summary, we confirmed the nonlinear relation between thickness and Young's modulus measured by SWE in thin layer samples, and offered a simple and practical correction strategy which is convenient for clinicians to use. PMID:27588234

  2. 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.

  3. The need for continuous and comprehensive sampling of effort/response bias during neuropsychological examinations.

    PubMed

    Boone, Kyle Brauer

    2009-05-01

    While most neuropsychologists are now administering measures of response bias in neuropsychological evaluations, it is still likely that detection of non-credible test performance is inadequate due to faulty assumptions regarding poor effort, namely that it remains constant across a battery of tests. Four cases are described that illustrate the variability in negative response bias that occurs during neuropsychological evaluations; if effort had not been periodically sampled with heterogeneous types of effort indicators during these examinations, the suspect performance would not have been detected. These examples argue for both continuous and comprehensive sampling of effort, specifically that negative response bias be routinely monitored throughout neuropsychological evaluations, and that effort indicators involving differing cognitive abilities be employed to assess for feigning of selective deficits. PMID:18949583

  4. 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

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

    PubMed

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

    2015-05-01

    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

  6. 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

  7. 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. PMID:26931140

  8. 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

  9. 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. PMID:25025342

  10. 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.

  11. 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.

  12. 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

  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. Sample-to-sample variations and biases in estimates of two-point correlation functions

    NASA Astrophysics Data System (ADS)

    Itoh, Makoto; Suginohara, Tatsushi; Suto, Yasushi

    1992-10-01

    A quantitative estimate of the sample-to-sample variations of two-point correlation functions was obtained by extracting subsamples from N-body simulation data, and the extent to which these subsamples reproduce the correlation functions estimated from the entire data was examined. The method used was more direct than that used in the studies of Barrow et al. (1984) and Ling et al. (1986): rather than estimating the variations of the correlation functions from pseudosamples which were created from single data sets as has been done in the previous investigations, several independent ensembles with different geometries were created in the present study. Thus, the problem was assessed more quantitatively and precisely.

  15. 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

  16. 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. PMID:23389437

  17. 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.

  18. 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. PMID:23457462

  19. 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.

  20. 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.

  1. Adjusting for Attrition in School-Based Samples: Bias, Precision, and Cost Trade-Offs of Three Methods.

    ERIC Educational Resources Information Center

    McGuigan, K. A.; Ellickson, P. L.; Hays, R. D.; Bell, R. M.

    1997-01-01

    Tracking and two statistical methods (probability weighting and sample selection modeling) were studied as ways to minimize bias attributable to sample attrition in school-based studies. Data on student smoking from 30 middle schools illustrate that sample weighting yields the best results, with estimates superior to sample selection and much less…

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

    PubMed Central

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

    2015-01-01

    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. 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. PMID:25705052

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

    PubMed Central

    2015-01-01

    Abstract Background 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. New information 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

  4. 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. PMID:26871142

  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. Inverse propensity weighting to adjust for bias in fatal crash samples

    PubMed Central

    Clark, David E.; Hannan, Edward L.

    2012-01-01

    Background The Fatality Analysis Reporting System (FARS) has data from all areas of the United States, but is limited to fatal crashes. The National Automotive Sampling System – General Estimates System (NASS-GES) includes all types of serious traffic crashes, but is limited to a few sampling areas. Combining the strengths of these two samples might offset their limitations. Methods Logistic regression (allowing for sample design, and conditional upon selected person-, event-, and geographic-level factors) was used to determine the propensity (PFC) for each injured person in 2002–2008 NASS-GES data to be in a fatal crash sample. NASS-GES subjects injured in fatal crashes were then reweighted by a factor of WFC = (1/PFC) to create a “pseudopopulation”. The weights (WFC) derived from NASS-GES were also applied to injured subjects in 2007 FARS data to create another pseudopopulation. Characteristics and mortality predictions from these artificial pseudopopulations were compared to those obtained using the original NASS-GES sample. The sum of WFC for FARS cases was also used to estimate the number of crash injuries for rural and urban locations, and compared to independently reported data. Results Compared to regression results using the original NASS-GES sample, unadjusted models based on fatal crash samples gave inaccurate estimates of covariate effects on mortality for injured subjects. After reweighting using WFC, estimates based upon the pseudopopulations were similar to results obtained using the original NASS-GES sample. The sum of WFC for FARS cases gave reasonable estimates for the number of crash injuries in rural and urban locations, and provided an estimate of the rural effect on mortality after controlling for other factors. Conclusions Weights derived from analysis of NASS-GES data (the inverse propensity for selection into a fatal crash sample) allow appropriate adjustment for selection bias in fatal crash samples, including FARS. PMID:23084095

  7. 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.

  8. 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.

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

    PubMed

    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

  10. 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

  11. Augmented composite likelihood for copula modeling in family studies under biased sampling.

    PubMed

    Zhong, Yujie; Cook, Richard J

    2016-07-01

    The heritability of chronic diseases can be effectively studied by examining the nature and extent of within-family associations in disease onset times. Families are typically accrued through a biased sampling scheme in which affected individuals are identified and sampled along with their relatives who may provide right-censored or current status data on their disease onset times. We develop likelihood and composite likelihood methods for modeling the within-family association in these times through copula models in which dependencies are characterized by Kendall's [Formula: see text] Auxiliary data from independent individuals are exploited by augmentating composite likelihoods to increase precision of marginal parameter estimates and consequently increase efficiency in dependence parameter estimation. An application to a motivating family study in psoriatic arthritis illustrates the method and provides some evidence of excessive paternal transmission of risk. PMID:26819481

  12. 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

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

    PubMed

    Starrfelt, Jostein; Liow, Lee Hsiang

    2016-04-01

    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

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

    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.

  16. 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

  17. The perils of straying from protocol: sampling bias and interviewer effects.

    PubMed

    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

  18. Sample preparation bias in carbon stable isotope ratio analysis of fruit juices and sweeteners.

    PubMed

    Krueger, D A

    1993-01-01

    Two sample preparation methods are commonly used for carbon stable isotope ratio analysis (SIRA). One involves combustion of the sample with oxygen at 850 degrees C; the other involves combustion of the sample with CuO in an evacuated glass tube at 550 degrees C. I observed in our laboratory that these 2 methods yield different results for sugar-based products such as fruit juices, sweeteners, and vanillin. The CuO method yields results approximately 1%. more positive than the oxygen combustion method. This bias is also observed in other laboratories, as shown in an analysis of the results of the AOAC collaborative studies of carbon SIRA of maple syrup, orange juice, honey, and honey protein. The oxygen combustion method is the AOAC method for honey, apple juice, and orange juice; both methods are incorporated into the AOAC method for maple syrup. I recommend that data generated by the CuO combustion method be appropriately corrected to yield results concordant with the official oxygen combustion method. PMID:8471867

  19. 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.

  20. Biased sampling of methane release from northern lakes: A problem for extrapolation

    NASA Astrophysics Data System (ADS)

    Wik, Martin; Thornton, Brett F.; Bastviken, David; Uhlbäck, Jo; Crill, Patrick M.

    2016-02-01

    Methane emissions from lakes are widely thought to be highly irregular and difficult to quantify with anything other than numerous distributed measurement stations and long-term sampling campaigns. In spite of this, a large majority of the study sites north of 50°N have been measured over surprisingly short time periods of only one to a few days. Using long-term data from three intensively studied small subarctic lakes, we recommend that measurements of diffusive methane flux and ebullition should be made over at least 11 and 39 days scattered throughout the ice-free season using depth-stratified sampling at 3 and 11 or more locations, respectively. We further show that low temporal and spatial resolutions are unlikely to cause overestimates. Therefore, we argue that most sites measured previously are likely underestimated in terms of emission potential. Avoiding these biases seen in much of the contemporary data is crucial to further constrain large-scale methane emissions from northern lakes and ponds.

  1. 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.

  2. Inertial particle acceleration statistics in turbulence: Effects of filtering, biased sampling, and flow topology

    NASA Astrophysics Data System (ADS)

    Salazar, Juan P. L. C.; Collins, Lance R.

    2012-08-01

    In this study, we investigate the effect of "biased sampling," i.e., the clustering of inertial particles in regions of the flow with low vorticity, and "filtering," i.e., the tendency of inertial particles to attenuate the fluid velocity fluctuations, on the probability density function of inertial particle accelerations. In particular, we find that the concept of "biased filtering" introduced by Ayyalasomayajula et al. ["Modeling inertial particle acceleration statistics in isotropic turbulence," Phys. Fluids 20, 0945104 (2008), 10.1063/1.2976174], in which particles filter stronger acceleration events more than weaker ones, is relevant to the higher order moments of acceleration. Flow topology and its connection to acceleration is explored through invariants of the velocity-gradient, strain-rate, and rotation-rate tensors. A semi-quantitative analysis is performed where we assess the contribution of specific flow topologies to acceleration moments. Our findings show that the contributions of regions of high vorticity and low strain decrease significantly with Stokes number, a non-dimensional measure of particle inertia. The contribution from regions of low vorticity and high strain exhibits a peak at a Stokes number of approximately 0.2. Following the methodology of Ooi et al. ["A study of the evolution and characteristics of the invariants of the velocity-gradient tensor in isotropic turbulence," J. Fluid Mech. 381, 141 (1999), 10.1017/S0022112098003681], we compute mean conditional trajectories in planes formed by pairs of tensor invariants in time. Among the interesting findings is the existence of a stable focus in the plane formed by the second invariants of the strain-rate and rotation-rate tensors. Contradicting the results of Ooi et al., we find a stable focus in the plane formed by the second and third invariants of the strain-rate tensor for fluid tracers. We confirm, at an even higher Reynolds number, the conjecture of Collins and Keswani ["Reynolds

  3. Ion beam deposition processes for improved hard bias magnetic and device properties in the abutted junction configuration

    NASA Astrophysics Data System (ADS)

    Devasahayam, Adrian J.; Wang, Jinsong; Hedge, Hari

    2000-05-01

    Permanent magnet films of Cr/CoCrPt for use in an abutted junction hard bias scheme were deposited by an ion beam deposition (IBD) system. The deposition angle control of IBD systems was employed to yield some excellent material and device related improvements. For films with the structure Cr-50 Å/CoCrPt-250 Å, increasing the deposition angle θ (as measured from the substrate normal) of the Cr layer from 20° to 60°, resulted in an increase in coercivity from 1860 to 1905 Oe. X-ray diffraction measurements showed that this improvement was related to an increase in CoCrPt in-plane texture and a decrease in c-axis perpendicular texture. The reason for this increase in in-plane texture is that there is better epitaxial matching between the CoCrPt and the Cr underlayer brought about by a change in the lattice dimension of Cr as a result of changing stress levels. Another positive effect of depositing the Cr at a larger angle is that the Cr would be thicker farther into the abutted junction and thus delay the onset of poor magnetic properties due to a thinning underlayer. The angle of deposition parameter can be used to further advantage by depositing the lead layer at a larger angle than the permanent magnet layers. This type of scheme would allow the leads to encroach over the permanent magnets and make direct contact with the sensor, yielding low contact resistance.

  4. 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.

  5. 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…

  6. 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.

  7. Sampling Soil CO2 for Isotopic Flux Partitioning: Non Steady State Effects and Methodological Biases

    NASA Astrophysics Data System (ADS)

    Snell, H. S. K.; Robinson, D.; Midwood, A. J.

    2014-12-01

    Measurements of δ13C of soil CO2 are used to partition the surface flux into autotrophic and heterotrophic components. Models predict that the δ13CO2 of the soil efflux is perturbed by non-steady state (NSS) diffusive conditions. These could be large enough to render δ13CO2 unsuitable for accurate flux partitioning. Field studies sometimes find correlations between efflux δ13CO2 and flux or temperature, or that efflux δ13CO2 is not correlated as expected with biological drivers. We tested whether NSS effects in semi-natural soil were comparable with those predicted. We compared chamber designs and their sensitivity to changes in efflux δ13CO2. In a natural soil mesocosm, we controlled temperature to generate NSS conditions of CO2 production. We measured the δ13C of soil CO2 using in situ probes to sample the subsurface, and dynamic and forced-diffusion chambers to sample the surface efflux. Over eight hours we raised soil temperature by 4.5 OC to increase microbial respiration. Subsurface CO2 concentration doubled, surface efflux became 13C-depleted by 1 ‰ and subsurface CO2 became 13C-enriched by around 2 ‰. Opposite changes occurred when temperature was lowered and CO2 production was decreasing. Different chamber designs had inherent biases but all detected similar changes in efflux δ13CO2, which were comparable to those predicted. Measurements using dynamic chambers were more 13C-enriched than expected, probably due to advection of CO2 into the chamber. In the mesocosm soil, δ13CO2 of both efflux and subsurface was determined by physical processes of CO2 production and diffusion. Steady state conditions are unlikely to prevail in the field, so spot measurements of δ13CO2 and assumptions based on the theoretical 4.4 ‰ diffusive fractionation will not be accurate for estimating source δ13CO2. Continuous measurements could be integrated over a period suitable to reduce the influence of transient NSS conditions. It will be difficult to disentangle

  8. 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

  9. 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/.

  10. 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…

  11. Does volumetric absorptive microsampling eliminate the hematocrit bias for caffeine and paraxanthine in dried blood samples? A comparative study.

    PubMed

    De Kesel, Pieter M M; Lambert, Willy E; Stove, Christophe P

    2015-06-30

    Volumetric absorptive microsampling (VAMS) is a novel sampling technique that allows the straightforward collection of an accurate volume of blood (approximately 10μL) from a drop or pool of blood by dipping an absorbent polymeric tip into it. The resulting blood microsample is dried and analyzed as a whole. The aim of this study was to evaluate the potential of VAMS to overcome the hematocrit bias, an important issue in the analysis of dried blood microsamples. An LC-MS/MS method for analysis of the model compounds caffeine and paraxanthine in VAMS samples was fully validated and fulfilled all pre-established criteria. In conjunction with previously validated procedures for dried blood spots (DBS) and blood, this allowed us to set up a meticulous comparative study in which both compounds were determined in over 80 corresponding VAMS, DBS and liquid whole blood samples. These originated from authentic human patient samples, covering a wide hematocrit range (0.21-0.50). By calculating the differences with reference whole blood concentrations, we found that analyte concentrations in VAMS samples were not affected by a bias that changed over the evaluated hematocrit range, in contrast to DBS results. However, VAMS concentrations tend to overestimate whole blood concentrations, as a consistent positive bias was observed. A different behavior of VAMS samples prepared from incurred and spiked blood, combined with a somewhat reduced recovery of caffeine and paraxanthine from VAMS tips at high hematocrit values, an effect that was not observed for DBS using a very similar extraction procedure, was found to be at the basis of the observed VAMS-whole blood deviations. Based on this study, being the first in which the validity and robustness of VAMS is evaluated by analyzing incurred human samples, it can be concluded that VAMS effectively assists in eliminating the effect of hematocrit. PMID:26041521

  12. Samples from subdivided populations yield biased estimates of effective size that overestimate the rate of loss of genetic variation

    PubMed Central

    Ryman, Nils; Allendorf, Fred W; Jorde, Per Erik; Laikre, Linda; Hössjer, Ola

    2014-01-01

    Many empirical studies estimating effective population size apply the temporal method that provides an estimate of the variance effective size through the amount of temporal allele frequency change under the assumption that the study population is completely isolated. This assumption is frequently violated, and the magnitude of the resulting bias is generally unknown. We studied how gene flow affects estimates of effective size obtained by the temporal method when sampling from a population system and provide analytical expressions for the expected estimate under an island model of migration. We show that the temporal method tends to systematically underestimate both local and global effective size when populations are connected by gene flow, and the bias is sometimes dramatic. The problem is particularly likely to occur when sampling from a subdivided population where high levels of gene flow obscure identification of subpopulation boundaries. In such situations, sampling in a manner that prevents biased estimates can be difficult. This phenomenon might partially explain the frequently reported unexpectedly low effective population sizes of marine populations that have raised concern regarding the genetic vulnerability of even exceptionally large populations. PMID:24034449

  13. 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.

  14. 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

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

    PubMed

    Wang, Kaicun

    2014-01-01

    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. PMID:24717688

  16. 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.

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

    NASA Astrophysics Data System (ADS)

    Wang, K.

    2014-12-01

    Global mean surface air temperature have risen by 0.74 °C over the last 100 years. However, the definition of mean surface air temperature 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 temperatures (Td1) over land have been taken to be the average of the daily maximum and minimum temperature measurements. All existing principle global temperature analyses over land are primarily based on Td1. Here, I make a first quantitative assessment of the bias in the use of Td1 to estimate trends of mean air temperature using hourly air temperature 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 air temperature datasets based on Td1 to examine spatial patterns of global warming.

  18. Alleviating Linear Ecological Bias and Optimal Design with Sub-sample Data

    PubMed Central

    Glynn, Adam; Wakefield, Jon; Handcock, Mark S.; Richardson, Thomas S.

    2009-01-01

    Summary In this paper, we illustrate that combining ecological data with subsample data in situations in which a linear model is appropriate provides three main benefits. First, by including the individual level subsample data, the biases associated with linear ecological inference can be eliminated. Second, by supplementing the subsample data with ecological data, the information about parameters will be increased. Third, we can use readily available ecological data to design optimal subsampling schemes, so as to further increase the information about parameters. We present an application of this methodology to the classic problem of estimating the effect of a college degree on wages. We show that combining ecological data with subsample data provides precise estimates of this value, and that optimal subsampling schemes (conditional on the ecological data) can provide good precision with only a fraction of the observations. PMID:20052294

  19. 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 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.

  20. 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.

  1. 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.…

  2. 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; 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.

  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. PMID:25062041

  4. Biases associated with several sampling methods used to estimate abundance of Ixodes scapularis and Amblyomma americanum (Acari: Ixodidae).

    PubMed

    Schulze, T L; Jordan, R A; Hung, R W

    1997-11-01

    Several tick sampling methods were evaluated for ixodes scapularis Say and Amblyomma americanum (I.) in oak-dominated mixed hard-wood, pitch pine-dominated, and mixed hardwood and pine forests in coastal New Jersey. Walking surveys were more efficient for collecting I. scapularis adults than dragging by a factor of > 2:1. In contrast, drag sampling yielded nearly twice as many A. americanum adults compared with walking surveys. I. scapularis subadults were rarely collected during walking surveys. A. americanum nymphs were collected from drags approximately 3:1 over walking surveys. Twice as many A. americanum larvae were obtained from drags compared with walking surveys. All developmental stages of A. americanum responded positively to carbon dioxide. Pitfall traps and leaf litter samples collected very few ticks. Tick distribution among habitats varied significantly with the sampling method chosen, and the relative ranking of sites with respect to tick abundance varied depending on the stage of tick sampled. Failure to recognize the biases in these commonly used sampling techniques can potentially lead to incorrect conclusions that can have significant adverse public health consequences. PMID:9439115

  5. 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

  6. A novel approach to non-biased systematic random sampling: A stereologic estimate of Purkinje cells in the human cerebellum

    PubMed Central

    Agashiwala, Rajiv M.; Louis, Elan D.; Hof, Patrick R.; Perl, Daniel P.

    2010-01-01

    Non-biased systematic sampling using the principles of stereology provides accurate quantitative estimates of objects within neuroanatomic structures. However, the basic principles of stereology are not optimally suited for counting objects that selectively exist within a limited but complex and convoluted portion of the sample, such as occurs when counting cerebellar Purkinje cells. In an effort to quantify Purkinje cells in association with certain neurodegenerative disorders, we developed a new method for stereologic sampling of the cerebellar cortex, involving calculating the volume of the cerebellar tissues, identifying and isolating the Purkinje cell layer and using this information to extrapolate non-biased systematic sampling data to estimate the total number of Purkinje cells in the tissues. Using this approach, we counted Purkinje cells in the right cerebella of four human male control specimens, aged 41, 67, 70 and 84 years, and estimated the total Purkinje cell number for the four entire cerebella to be 27.03, 19.74, 20.44 and 22.03 million cells, respectively. The precision of the method is seen when comparing the density of the cells within the tissue: 266,274, 173,166, 167,603 and 183,575 cells/cm3, respectively. Prior literature documents Purkinje cell counts ranging from 14.8 to 30.5 million cells. These data demonstrate the accuracy of our approach. Our novel approach, which offers an improvement over previous methodologies, is of value for quantitative work of this nature. This approach could be applied to morphometric studies of other similarly complex tissues as well. PMID:18725208

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

    SciTech Connect

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

    2005-05-15

    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 (T{sub c}) niobium-based monolithic SQUID sensors are mounted on the tip of a sapphire and thermally anchored to the helium reservoir. A 25 {mu}m 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 100 {mu}m, 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-T{sub c} niobium bare SQUID sensor, with an effective diameter of 80 {mu}m, and achieved a field sensitivity of 1.5 pT/Hz{sup 1/2} and a magnetic moment sensitivity of 5.4x10{sup -18} A m{sup 2}/Hz{sup 1/2} at a sensor-to-sample spacing of 100 {mu}m in the white noise region for frequencies above 100 Hz. 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-T{sub c} niobium multiloop SQUID sensor, with sensor sizes ranging from 250 {mu}m to 1 mm, and achieved sensitivities of 480-180 fT/Hz{sup 1/2} in the white noise region for frequencies above 100 Hz, 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

  8. Small sample performance of bias-corrected sandwich estimators for cluster-randomized trials with binary outcomes.

    PubMed

    Li, Peng; Redden, David T

    2015-01-30

    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 because of fewer assumptions and robustness to the misspecification of the covariance structure. PMID:25345738

  9. 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. PMID:23869450

  10. Configuration-Space Sampling in Potential Energy Surface Fitting: A Space-Reduced Bond-Order Grid Approach.

    PubMed

    Rampino, Sergio

    2016-07-14

    Potential energy surfaces (PESs) for use in dynamics calculations of few-atom reactive systems are commonly modeled as functional forms fitting or interpolating a set of ab initio energies computed at many nuclear configurations. An automated procedure is here proposed for optimal configuration-space sampling in generating this set of energies as part of the grid-empowered molecular simulator GEMS (Laganà et al., J. Grid Comput. 2010, 8, 571-586). The scheme is based on a space-reduced formulation of the so-called bond-order variables allowing for a balanced representation of the attractive and repulsive regions of a diatom configuration space. Uniform grids based on space-reduced bond-order variables are proven to outperform those defined on the more conventional bond-length variables in converging the fitted/interpolated PES to the computed ab initio one with increasing number of grid points. Benchmarks are performed on the one- and three-dimensional prototype systems H2 and H3 using both a local-interpolation (modified Shepard) and a global-fitting (Aguado-Paniagua) scheme. PMID:26674105

  11. 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

  12. 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.

  13. 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

    2016-01-01

    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. PMID:26751471

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

    PubMed Central

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

    2016-01-01

    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. PMID:26751471

  15. 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. PMID:25311212

  16. 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…

  17. 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…

  18. 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

    2016-06-01

    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. PMID:26946052

  19. 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

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

    PubMed

    Vaganay, Arnaud

    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

  1. 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. PMID:22235175

  2. 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

  3. 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.

  4. Implicit and explicit anti-fat bias among a large sample of medical doctors by BMI, race/ethnicity and gender.

    PubMed

    Sabin, Janice A; Marini, Maddalena; Nosek, Brian A

    2012-01-01

    Overweight patients report weight discrimination in health care settings and subsequent avoidance of routine preventive health care. The purpose of this study was to examine implicit and explicit attitudes about weight among a large group of medical doctors (MDs) to determine the pervasiveness of negative attitudes about weight among MDs. Test-takers voluntarily accessed a public Web site, known as Project Implicit®, and opted to complete the Weight Implicit Association Test (IAT) (N = 359,261). A sub-sample identified their highest level of education as MD (N = 2,284). Among the MDs, 55% were female, 78% reported their race as white, and 62% had a normal range BMI. This large sample of test-takers showed strong implicit anti-fat bias (Cohen's d = 1.0). MDs, on average, also showed strong implicit anti-fat bias (Cohen's d = 0.93). All test-takers and the MD sub-sample reported a strong preference for thin people rather than fat people or a strong explicit anti-fat bias. We conclude that strong implicit and explicit anti-fat bias is as pervasive among MDs as it is among the general public. An important area for future research is to investigate the association between providers' implicit and explicit attitudes about weight, patient reports of weight discrimination in health care, and quality of care delivered to overweight patients. PMID:23144885

  5. Implicit and Explicit Anti-Fat Bias among a Large Sample of Medical Doctors by BMI, Race/Ethnicity and Gender

    PubMed Central

    Sabin, Janice A.; Marini, Maddalena; Nosek, Brian A.

    2012-01-01

    Overweight patients report weight discrimination in health care settings and subsequent avoidance of routine preventive health care. The purpose of this study was to examine implicit and explicit attitudes about weight among a large group of medical doctors (MDs) to determine the pervasiveness of negative attitudes about weight among MDs. Test-takers voluntarily accessed a public Web site, known as Project Implicit®, and opted to complete the Weight Implicit Association Test (IAT) (N = 359,261). A sub-sample identified their highest level of education as MD (N = 2,284). Among the MDs, 55% were female, 78% reported their race as white, and 62% had a normal range BMI. This large sample of test-takers showed strong implicit anti-fat bias (Cohen’s d = 1.0). MDs, on average, also showed strong implicit anti-fat bias (Cohen’s d = 0.93). All test-takers and the MD sub-sample reported a strong preference for thin people rather than fat people or a strong explicit anti-fat bias. We conclude that strong implicit and explicit anti-fat bias is as pervasive among MDs as it is among the general public. An important area for future research is to investigate the association between providers’ implicit and explicit attitudes about weight, patient reports of weight discrimination in health care, and quality of care delivered to overweight patients. PMID:23144885

  6. 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.

  7. 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.

  8. 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. PMID:24745750

  9. 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...

  10. 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. PMID:26475937

  11. The composite effect for inverted faces is reliable at large sample sizes and requires the basic face configuration.

    PubMed

    Susilo, Tirta; Rezlescu, Constantin; Duchaine, Bradley

    2013-01-01

    The absence of the face composite effect (FCE) for inverted faces is often considered evidence that holistic processing operates only on upright faces. However, such absence might be explained by power issues: Most studies that have failed to find the inverted FCE tested 24 participants or less. Here we find that the inverted FCE exists reliably when we tested at least 60 participants. The inverted FCE was ∼ 18% the size of the upright FCE, and it was unaffected by testing order: It did not matter whether participants did the upright condition first (Experiment 1, n = 64) or the inverted condition first (Experiment 2, n = 68). The effect also remained when upright and inverted trials were mixed (Experiment 3, n = 60). An individual differences analysis found a modest positive correlation between inverted and upright FCE, suggesting partially shared mechanisms. A critical control experiment demonstrates that the inverted FCE cannot be explained by visuospatial attention or other generic accounts because the effect disappeared when the basic face configuration was disrupted (Experiment 4, n = 50). Our study shows that the inverted FCE is a reliable effect that requires an intact face configuration, consistent with the notion that some holistic processing also operates on inverted faces. PMID:24222184

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

    PubMed Central

    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 (FST and DC) 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 DC, 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. PMID:26989639

  13. 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. PMID:26989639

  14. 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

  15. Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges

    PubMed Central

    Hardoim, Cristiane C. P.; Cardinale, Massimiliano; Cúcio, Ana C. B.; Esteves, Ana I. S.; Berg, Gabriele; Xavier, Joana R.; Cox, Cymon J.; Costa, Rodrigo

    2014-01-01

    Complex and distinct bacterial communities inhabit marine sponges and are believed to be essential to host survival, but our present-day inability to domesticate sponge symbionts in the laboratory hinders our access to the full metabolic breadth of these microbial consortia. We address bacterial cultivation bias in marine sponges using a procedure that enables direct comparison between cultivated and uncultivated symbiont community structures. Bacterial community profiling of the sympatric keratose species Sarcotragus spinosulus and Ircinia variabilis (Dictyoceratida, Irciniidae) was performed by polymerase chain reaction-denaturing gradient gel electrophoresis and 454-pyrosequecing of 16S rRNA gene fragments. Whereas cultivation-independent methods revealed species-specific bacterial community structures in these hosts, cultivation-dependent methods resulted in equivalent community assemblages from both species. Between 15 and 18 bacterial phyla were found in S. spinosulus and I. variabilis using cultivation-independent methods. However, Alphaproteobacteria and Gammaproteobacteria dominated the cultivation-dependent bacterial community. While cultivation-independent methods revealed about 200 and 220 operational taxonomic units (OTUs, 97% gene similarity) in S. spinosulus and I. variabilis, respectively, only 33 and 39 OTUs were found in these species via culturing. Nevertheless, around 50% of all cultured OTUs escaped detection by cultivation-independent methods, indicating that standard cultivation makes otherwise host-specific bacterial communities similar by selectively enriching for rarer and generalist symbionts. This study sheds new light on the diversity spectrum encompassed by cultivated and uncultivated sponge-associated bacteria. Moreover, it highlights the need to develop alternative culturing technologies to capture the dominant sponge symbiont fraction that currently remains recalcitrant to laboratory manipulation. PMID:25477868

  16. Conformational sampling of oligosaccharides using Hamiltonian replica exchange with two-dimensional dihedral biasing potentials and the weighted histogram analysis method (WHAM).

    PubMed

    Yang, Mingjun; MacKerel, Alexander D

    2015-02-10

    Oligosaccharides and polysaccharides exert numerous functional roles in biology through their structural diversity and conformational properties. To investigate their conformational properties using computational methods, Hamiltonian replica exchange (H-REX) combined with two-dimensional grid-based correction maps as biasing potentials (bpCMAP) significantly improves the sampling efficiency about glycosidic linkages. In the current study, we extend the application of H-REX with bpCMAP to complex saccharides and establish systematic procedures for bpCMAP construction, determination of replica distribution, and data analysis. Our main findings are that (1) the bpCMAP for each type of glycosidic linkage can be constructed from the corresponding disaccharide using gas-phase umbrella sampling simulations, (2) the replica distribution can be conveniently determined following the exact definition of the average acceptance ratio based on the assigned distribution of biasing potentials, and (3) the extracted free energy surface (or potential of mean force (PMF)) can be improved using the weighted histogram analysis method (WHAM) allowing for the inclusion of data from the excited state replicas in the calculated probability distribution. The method is applied to a branched N-glycan found on the HIV gp120 protein, and a linear N-glycan. Considering the general importance of N-glycans and the wide appreciation of the sampling problem, the present method represents an efficient procedure for the conformational sampling of complex oligo- and polysaccharides under explicit solvent conditions. More generally, the use of WHAM is anticipated to be of general utility for the calculation of PMFs from H-REX simulations in a wide range of macromolecular systems. PMID:25705140

  17. DMD-based software-configurable spatially-offset Raman spectroscopy for spectral depth-profiling of optically turbid samples.

    PubMed

    Liao, Zhiyu; Sinjab, Faris; Gibson, Graham; Padgett, Miles; Notingher, Ioan

    2016-06-13

    Spectral depth-profiling of optically turbid samples is of high interest to a broad range of applications. We present a method for measuring spatially-offset Raman spectroscopy (SORS) over a range of length scales by incorporating a digital micro-mirror device (DMD) into a sample-conjugate plane in the detection optical path. The DMD can be arbitrarily programmed to collect/reject light at spatial positions in the 2D sample-conjugate plane, allowing spatially offset Raman measurements. We demonstrate several detection geometries, including annular and simultaneous multi-offset modalities, for both macro- and micro-SORS measurements, all on the same instrument. Compared to other SORS modalities, DMD-based SORS provides more flexibility with only minimal additional experimental complexity for subsurface Raman collection. PMID:27410290

  18. 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. PMID:11752497

  19. 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

  20. 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.

  1. 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

  2. Mapping Transmission Risk of Lassa Fever in West Africa: The Importance of Quality Control, Sampling Bias, and Error Weighting

    PubMed Central

    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. PMID:25105746

  3. 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. PMID:25105746

  4. 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

  5. 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

  6. Sympathetic bias.

    PubMed

    Levy, David M; Peart, Sandra J

    2008-06-01

    We wish to deal with investigator bias in a statistical context. We sketch how a textbook solution to the problem of "outliers" which avoids one sort of investigator bias, creates the temptation for another sort. We write down a model of the approbation seeking statistician who is tempted by sympathy for client to violate the disciplinary standards. We give a simple account of one context in which we might expect investigator bias to flourish. Finally, we offer tentative suggestions to deal with the problem of investigator bias which follow from our account. As we have given a very sparse and stylized account of investigator bias, we ask what might be done to overcome this limitation. PMID:17925315

  7. Hindsight Bias.

    PubMed

    Roese, Neal J; Vohs, Kathleen D

    2012-09-01

    Hindsight bias occurs when people feel that they "knew it all along," that is, when they believe that an event is more predictable after it becomes known than it was before it became known. Hindsight bias embodies any combination of three aspects: memory distortion, beliefs about events' objective likelihoods, or subjective beliefs about one's own prediction abilities. Hindsight bias stems from (a) cognitive inputs (people selectively recall information consistent with what they now know to be true and engage in sensemaking to impose meaning on their own knowledge), (b) metacognitive inputs (the ease with which a past outcome is understood may be misattributed to its assumed prior likelihood), and (c) motivational inputs (people have a need to see the world as orderly and predictable and to avoid being blamed for problems). Consequences of hindsight bias include myopic attention to a single causal understanding of the past (to the neglect of other reasonable explanations) as well as general overconfidence in the certainty of one's judgments. New technologies for visualizing and understanding data sets may have the unintended consequence of heightening hindsight bias, but an intervention that encourages people to consider alternative causal explanations for a given outcome can reduce hindsight bias. PMID:26168501

  8. 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. PMID:26085130

  9. Low-resolution Spectroscopy of Gamma-ray Burst Optical Afterglows: Biases in the Swift Sample and Characterization of the Absorbers

    NASA Astrophysics Data System (ADS)

    Fynbo, J. P. U.; Jakobsson, P.; Prochaska, J. X.; Malesani, D.; Ledoux, C.; de Ugarte Postigo, A.; Nardini, M.; Vreeswijk, P. M.; Wiersema, K.; Hjorth, J.; Sollerman, J.; Chen, H.-W.; Thöne, C. C.; Björnsson, G.; Bloom, J. S.; Castro-Tirado, A. J.; Christensen, L.; De Cia, A.; Fruchter, A. S.; Gorosabel, J.; Graham, J. F.; Jaunsen, A. O.; Jensen, B. L.; Kann, D. A.; Kouveliotou, C.; Levan, A. J.; Maund, J.; Masetti, N.; Milvang-Jensen, B.; Palazzi, E.; Perley, D. A.; Pian, E.; Rol, E.; Schady, P.; Starling, R. L. C.; Tanvir, N. R.; Watson, D. J.; Xu, D.; Augusteijn, T.; Grundahl, F.; Telting, J.; Quirion, P.-O.

    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 Lyα 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., γ-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 γ-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 βOX < 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 to a bias against the

  10. 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

    2015-11-01

    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. PMID:26483469

  11. Biased Brownian dynamics for rate constant calculation.

    PubMed

    Zou, G; Skeel, R D; Subramaniam, S

    2000-08-01

    An enhanced sampling method-biased Brownian dynamics-is developed for the calculation of diffusion-limited biomolecular association reaction rates with high energy or entropy barriers. Biased Brownian dynamics introduces a biasing force in addition to the electrostatic force between the reactants, and it associates a probability weight with each trajectory. A simulation loses weight when movement is along the biasing force and gains weight when movement is against the biasing force. The sampling of trajectories is then biased, but the sampling is unbiased when the trajectory outcomes are multiplied by their weights. With a suitable choice of the biasing force, more reacted trajectories are sampled. As a consequence, the variance of the estimate is reduced. In our test case, biased Brownian dynamics gives a sevenfold improvement in central processing unit (CPU) time with the choice of a simple centripetal biasing force. PMID:10919998

  12. 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.

  13. Reducing Bias Amplification in the Presence of Unmeasured Confounding Through Out-of-Sample Estimation Strategies for the Disease Risk Score

    PubMed Central

    Wyss, Richard; Lunt, Mark; Brookhart, M. Alan; Glynn, Robert J.; Stürmer, Til

    2014-01-01

    The prognostic score, or disease risk score (DRS), is a summary score that is used to control for confounding in non-experimental studies. While the DRS has been shown to effectively control for measured confounders, unmeasured confounding continues to be a fundamental obstacle in non-experimental research. Both theory and simulations have shown that in the presence of unmeasured confounding, controlling for variables that affect treatment (both instrumental variables and measured confounders) amplifies the bias caused by unmeasured confounders. In this paper, we use causal diagrams and path analysis to review and illustrate the process of bias amplification. We show that traditional estimation strategies for the DRS do not avoid bias amplification when controlling for predictors of treatment. We then discuss estimation strategies for the DRS that can potentially reduce bias amplification that is caused by controlling both instrumental variables and measured confounders. We show that under certain assumptions, estimating the DRS in populations outside the defined study cohort where treatment has not been introduced, or in outside populations with reduced treatment prevalence can control for the confounding effects of measured confounders while at the same time reduce bias amplification. PMID:25313347

  14. 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

  15. 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

  16. Fingernail Configuration

    PubMed Central

    Jung, Jin Woo; Shin, Jun Ho; Kwon, Yu Jin; Hwang, Jae Ha; Lee, Sam Yong

    2015-01-01

    Background A number of conditions can alter a person's fingernail configuration. The ratio between fingernail width and length (W/L) is an important aesthetic criterion, and some underlying diseases can alter the size of the fingernail. Fingernail curvature can be altered by systemic disorders or disorders of the fingernail itself. Although the shape and curvature of the fingernail can provide diagnostic clues for various diseases, few studies have precisely characterized normal fingernail configuration. Methods We measured the W/L ratio of the fingernail, transverse fingernail curvature, hand length, hand breadth, and distal interphalangeal joint width in 300 volunteers with healthy fingernails. We also investigated whether age, sex, height, and handedness influenced the fingernail W/L ratio and transverse fingernail curvature. Results In women, fingernail W/L ratios were similar across all five fingers, and were lower than those in men. The highest value of transverse fingernail curvature was found in the thumb, followed by the index, middle, ring, and little fingers. Handedness and aging influenced transverse fingernail curvature, but not the fingernail W/L ratio. Fingernails were flatter on the dominant hand than on the non-dominant hand. The radius of transverse fingernail curvature increased with age, indicating that fingernails tended to flatten with age. Conclusions Our quantitative data on fingernail configuration can be used as a reference range for diagnosing various diseases and deformities of the fingernail, and for performing reconstructive or aesthetic fingernail surgery. PMID:26618124

  17. Biased Allostery.

    PubMed

    Edelstein, Stuart J; Changeux, Jean-Pierre

    2016-09-01

    G-protein-coupled receptors (GPCRs) constitute a large group of integral membrane proteins that transduce extracellular signals from a wide range of agonists into targeted intracellular responses. Although the responses can vary depending on the category of G-proteins activated by a particular receptor, responses were also found to be triggered by interactions of the receptor with β-arrestins. It was subsequently discovered that for the same receptor molecule (e.g., the β-adrenergic receptor), some agonists have a propensity to specifically favor responses by G-proteins, others by β-arrestins, as has now been extensively studied. This feature of the GPCR system is known as biased agonism and is subject to various interpretations, including agonist-induced conformational change versus selective stabilization of preexisting active conformations. Here, we explore a complete allosteric framework for biased agonism based on alternative preexisting conformations that bind more strongly, but nonexclusively, either G-proteins or β-arrestins. The framework incorporates reciprocal effects among all interacting molecules. As a result, G-proteins and β-arrestins are in steric competition for binding to the cytoplasmic surface of either the G-protein-favoring or β-arrestin-favoring GPCR conformation. Moreover, through linkage relations, the strength of the interactions of G-proteins or β-arrestins with the corresponding active conformation potentiates the apparent affinity for the agonist, effectively equating these two proteins to allosteric modulators. The balance between response alternatives can also be influenced by the physiological concentrations of either G-proteins or β-arrestins, as well as by phosphorylation or interactions with positive or negative allosteric modulators. The nature of the interactions in the simulations presented suggests novel experimental tests to distinguish more fully among alternative mechanisms. PMID:27602718

  18. 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.

  19. 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

  20. 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.

  1. Quantitative trait locus (QTL) mapping using different testers and independent population samples in maize reveals low power of QTL detection and large bias in estimates of QTL effects.

    PubMed

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

    1998-05-01

    The efficiency of marker-assisted selection (MAS) depends on the power of quantitative trait locus (QTL) detection and unbiased estimation of QTL effects. Two independent samples N = 344 and 107 of F2 plants were genotyped for 89 RFLP markers. For each sample, testcross (TC) progenies of the corresponding F3 lines with two testers were evaluated in four environments. QTL for grain yield and other agronomically important traits were mapped in both samples. QTL effects were estimated from the same data as used for detection and mapping of QTL (calibration) and, based on QTL positions from calibration, from the second, independent sample (validation). For all traits and both testers we detected a total of 107 QTL with N = 344, and 39 QTL with N = 107, of which only 20 were in common. Consistency of QTL effects across testers was in agreement with corresponding genotypic correlations between the two TC series. Most QTL displayed no significant QTL x environment nor epistatic interactions. Estimates of the proportion of the phenotypic and genetic variance explained by QTL were considerably reduced when derived from the independent validation sample as opposed to estimates from the calibration sample. We conclude that, unless QTL effects are estimated from an independent sample, they can be inflated, resulting in an overly optimistic assessment of the efficiency of MAS. PMID:9584111

  2. 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…

  3. Angular bias errors in three-component laser velocimeter measurements

    SciTech Connect

    Chen, C.Y.; Kim, P.J.; Walker, D.T.

    1996-09-01

    For three-component laser velocimeter systems, the change in projected area of the coincident measurement volume for different flow directions will introduce an angular bias in naturally sampled data. In this study, the effect of turbulence level and orientation of the measurement volumes on angular bias errors was examined. The operation of a typical three-component laser velocimeter was simulated using a Monte Carlo technique. Results for the specific configuration examined show that for turbulence levels less than 10% no significant bias errors in the mean velocities will occur and errors in the root-mean-square (r.m.s.) velocities will be less than 3% for all orientations. For turbulence levels less than 30%, component mean velocity bias errors less than 5% of the mean velocity vector magnitude can be attained with proper orientation of the measurement volume; however, the r.m.s. velocities may be in error as much as 10%. For turbulence levels above 50%, there is no orientation which will yield accurate estimates of all three mean velocities; component mean velocity errors as large as 15% of the mean velocity vector magnitude may be encountered.

  4. 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.

  5. 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.

  6. 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…

  7. 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 PMID:26502203

  8. Bias in Grading

    ERIC Educational Resources Information Center

    Malouff, John

    2008-01-01

    Bias in grading can be conscious or unconscious. The author describes different types of bias, such as those based on student attractiveness or performance in prior courses, and a variety of methods of reducing bias, including keeping students anonymous during grading and using detailed criteria for subjective grading.

  9. Bias in Mental Tests.

    ERIC Educational Resources Information Center

    Bond, Lloyd

    1981-01-01

    While some forms of test bias (for example, bias in selection and prediction) appear amenable to definitional consensus, a definition of cultural bias will remain problematic so long as it is confused with the nature/nurture issue. (Author/BW)

  10. 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'…

  11. 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…

  12. 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…

  13. 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.

  14. 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.

  15. 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.

  16. 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. PMID:26386014

  17. Lagrangian bias in the local bias model

    SciTech Connect

    Frusciante, Noemi; Sheth, Ravi K. E-mail: sheth@ictp.it

    2012-11-01

    It is often assumed that the halo-patch fluctuation field can be written as a Taylor series in the initial Lagrangian dark matter density fluctuation field. We show that if this Lagrangian bias is local, and the initial conditions are Gaussian, then the two-point cross-correlation between halos and mass should be linearly proportional to the mass-mass auto-correlation function. This statement is exact and valid on all scales; there are no higher order contributions, e.g., from terms proportional to products or convolutions of two-point functions, which one might have thought would appear upon truncating the Taylor series of the halo bias function. In addition, the auto-correlation function of locally biased tracers can be written as a Taylor series in the auto-correlation function of the mass; there are no terms involving, e.g., derivatives or convolutions. Moreover, although the leading order coefficient, the linear bias factor of the auto-correlation function is just the square of that for the cross-correlation, it is the same as that obtained from expanding the mean number of halos as a function of the local density only in the large-scale limit. In principle, these relations allow simple tests of whether or not halo bias is indeed local in Lagrangian space. We discuss why things are more complicated in practice. We also discuss our results in light of recent work on the renormalizability of halo bias, demonstrating that it is better to renormalize than not. We use the Lognormal model to illustrate many of our findings.

  18. 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

  19. 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…

  20. Generalized Ellipsometry in Unusual Configurations

    SciTech Connect

    Jellison Jr, Gerald Earle; Holcomb, David Eugene; Hunn, John D; Rouleau, Christopher M; Wright, Gomez W

    2006-01-01

    Most ellipsometry experiments are performed by shining polarized light onto a sample at a large angle of incidence, and the results are interpreted in terms of thin film thicknesses and isotropic optical functions of the film or substrate. However, it is possible to alter the geometrical arrangement, either by observing the sample in transmission or at normal-incidence reflection. In both cases, the experiment is fundamentally the same, but the interpretation of the results is considerably different. Both configurations can be used in conjunction with microscope optics, allowing for images to be made of the sample. The results of three examples of these different configurations using the two-modulator generalized ellipsometer (2-MGE) are reported: (1) spectroscopic birefringence measurements of ZnO, (2) electric field-induced birefringence (Pockels effect) in GaAs, and (3) normal-incidence reflection anisotropy of highly oriented pyrolytic graphite (HOPG).

  1. 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. PMID:12848220

  2. 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.

  3. Harassment, Bias, and Discrimination.

    ERIC Educational Resources Information Center

    Welliver, Paul W.

    1995-01-01

    Discusses a new principle which has been added to the AECT (Association for Educational Communications and Technology) Code of Professional Ethics regarding discrimination, harassment, and bias. An example is presented which illustrates a violation of a professional colleague's rights. (LRW)

  4. 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.

  5. Racial and Ethnic Bias in Test Construction.

    ERIC Educational Resources Information Center

    Green, Donald Ross

    To determine if tryout samples typically used for item selection contribute to test bias against minority groups, item analyses were made of the California Achievement Tests using seven sub-groups of the standardization sample: Northern White Suburban, Northern Black Urban, Southern White Suburban, Southern Black Rural, Southern White Rural,…

  6. Political bias is tenacious.

    PubMed

    Ditto, Peter H; Wojcik, Sean P; Chen, Eric Evan; Grady, Rebecca Hofstein; Ringel, Megan M

    2015-01-01

    Duarte et al. are right to worry about political bias in social psychology but they underestimate the ease of correcting it. Both liberals and conservatives show partisan bias that often worsens with cognitive sophistication. More non-liberals in social psychology is unlikely to speed our convergence upon the truth, although it may broaden the questions we ask and the data we collect. PMID:26786070

  7. CD bias control on hole pattern

    NASA Astrophysics Data System (ADS)

    Koike, Kyohei; Hara, Arisa; Natori, Sakurako; Yamauchi, Shohei; Yamato, Masatoshi; Oyama, Kenichi; Yaegashi, Hidetami

    2016-03-01

    Gridded design rules[1] is major process in configuring logic circuit used 193-immersion lithography. In the scaling of grid patterning, we can make 10nm order line and space pattern by using multiple patterning techniques such as self-aligned multiple patterning (SAMP) and litho-etch- litho-etch (LELE)[2][3][5] . On the other hand, Line cut process has some error parameters such as pattern defect, placement error, roughness and X-Y CD bias with the decreasing scale. Especially roughness and X-Y CD bias are paid attention because it cause cut error and pattern defect. In this case, we applied some smoothing process to care hole roughness[4]. Each smoothing process showed different effect on X-Y CD bias. In this paper, we will report the pattern controllability comparison of trench and block + inverse. It include X-Y CD bias, roughness and process usability. Furthermore we will discuss optimum method focused on X-Y CD bias when we use additional process such as smoothing and shrink etching .

  8. 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)

  9. Collective opinion formation model under Bayesian updating and confirmation bias.

    PubMed

    Nishi, Ryosuke; Masuda, Naoki

    2013-06-01

    We propose a collective opinion formation model with a so-called confirmation bias. The confirmation bias is a psychological effect with which, in the context of opinion formation, an individual in favor of an opinion is prone to misperceive new incoming information as supporting the current belief of the individual. Our model modifies a Bayesian decision-making model for single individuals [M. Rabin and J. L. Schrag, Q. J. Econ. 114, 37 (1999)] for the case of a well-mixed population of interacting individuals in the absence of the external input. We numerically simulate the model to show that all the agents eventually agree on one of the two opinions only when the confirmation bias is weak. Otherwise, the stochastic population dynamics ends up creating a disagreement configuration (also called polarization), particularly for large system sizes. A strong confirmation bias allows various final disagreement configurations with different fractions of the individuals in favor of the opposite opinions. PMID:23848643

  10. Weight Bias in University Health Professions Students.

    PubMed

    Blanton, Cynthia; Brooks, Jennifer K; McKnight, Laura

    2016-01-01

    Negative attitudes toward people with high body weight have been documented in pre-professional health students, prompting concern that such feelings may manifest as poor patient care in professional practice. This study assessed weight bias in university students in the non-physician health professions. A convenience sample of 206 students completed an online survey composed of a validated 14-item scale (1-5 lowest to highest weight bias) and questions regarding personal experiences of weight bias. Respondents were grouped by discipline within graduate and undergraduate levels. Weight bias was present in a majority of respondents. Overall, the percentage of responses indicative of weight bias was 92.7%. The mean total score was 3.65. ± 0.52, and the rating exceeded 3 for all 14 scale descriptors of high-weight people. In graduate students, discipline had a significant main effect on total score (p=0.01), with lower scores in dietetics (3.17 ± 0.46) vs audiology/sign language/speech language pathology (3.84 ± 0.41) and physician assistant students (3.78 ± 0.51; p<0.05). These findings show that weight bias is prevalent in health professions students at a mountain west university. Well-controlled studies that track students into professional practice would help determine whether bias-reduction interventions in college improve provider behaviors and clinical outcomes. PMID:27585618

  11. Featural information is sufficient to produce a left cheek bias for happiness perception.

    PubMed

    Low, Jia Y; Lindell, Annukka K

    2016-08-01

    People perceive the left cheek as more emotionally expressive than the right. Both configural and featural information enable the evaluation of emotional expressions; whether they make equivalent contributions to the left cheek bias is undetermined. As scrambling faces disrupts configural processing whilst leaving featural information intact, we investigated whether configural information is necessary, or featural information is sufficient, to induce a left cheek bias for emotion perception. Eighty-one participants (65 F, 16 M) viewed two types of left and right cheek image pairs - normal, scrambled - and indicated which image appeared happier (half mirror-reversed to control for perceptual biases). Results indicated a left cheek bias for both normal and scrambled faces, irrespective of mirror reversal. As scrambling faces disrupts configural processing, the fact that the left cheek was perceived as more expressive even when scrambled confirms that differences between the cheeks' featural information are sufficient to induce the left cheek bias. PMID:27363004

  12. Prediction Bias and Selection Bias: An Empirical Analysis.

    ERIC Educational Resources Information Center

    Cahan, Sorel; Gamliel, Eyal

    2001-01-01

    Proposed a definition of selection bias and studied the empirical relation between prediction bias and selection bias with respect to prominent social groups. Results show that, although the two biases are related, the relation is not isomorphic. It is mediated by the selection ratio, and for most selection ratios, it is only moderate. (SLD)

  13. 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.

  14. 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

  15. Bias in Psychological Assessment: Heterosexism.

    ERIC Educational Resources Information Center

    Chernin, Jeffrey; Holden, Janice Miner; Chandler, Cynthia

    1997-01-01

    Explores heterosexist bias in seven widely used assessment instruments. Focuses on bias that is observable in the instruments themselves and in the ancillary materials. Describes three types of bias, how these biases manifest in various instruments, and makes recommendations for mental health practitioners and for professionals who develop…

  16. 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.

  17. 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.

  18. 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.

  19. Biased to Learn Language

    ERIC Educational Resources Information Center

    Sebastian-Galles, Nuria

    2007-01-01

    Some recent publications that explore the foundations of early language development are reviewed in this article. The review adopts the pivotal idea that infants' advancements are helped by the existence of different types of biases. The infant's discovery of the phonological properties of the language of the environment, as well as their learning…

  20. FEL phased array configurations

    NASA Astrophysics Data System (ADS)

    Shellan, Jeffrey B.

    1986-01-01

    The advantages and disadvantages of various phased array and shared aperture concepts for FEL configurations are discussed. Consideration is given to the characteristics of intra- and inter-micropulse phasing; intra-macropulse phasing; an internal coupled resonator configuration; and an injection locked oscillator array. The use of a master oscillator power amplifier (MOPA) configuration with multiple or single master oscillators for FELs is examined. The venetian blind, rotating plate, single grating, and grating rhomb shared aperture concepts are analyzed. It is noted that the shared aperture approach using a grating rhomb and the MOPA concept with a single master oscillator and a coupled resonator are useful for FEL phased array configurations; and the MOPA concept is most applicable.

  1. Composite biasing in Monte Carlo radiative transfer

    NASA Astrophysics Data System (ADS)

    Baes, Maarten; Gordon, Karl D.; Lunttila, Tuomas; Bianchi, Simone; Camps, Peter; Juvela, Mika; Kuiper, Rolf

    2016-05-01

    Biasing or importance sampling is a powerful technique in Monte Carlo radiative transfer, and can be applied in different forms to increase the accuracy and efficiency of simulations. One of the drawbacks of the use of biasing is the potential introduction of large weight factors. We discuss a general strategy, composite biasing, to suppress the appearance of large weight factors. We use this composite biasing approach for two different problems faced by current state-of-the-art Monte Carlo radiative transfer codes: the generation of photon packages from multiple components, and the penetration of radiation through high optical depth barriers. In both cases, the implementation of the relevant algorithms is trivial and does not interfere with any other optimisation techniques. Through simple test models, we demonstrate the general applicability, accuracy and efficiency of the composite biasing approach. In particular, for the penetration of high optical depths, the gain in efficiency is spectacular for the specific problems that we consider: in simulations with composite path length stretching, high accuracy results are obtained even for simulations with modest numbers of photon packages, while simulations without biasing cannot reach convergence, even with a huge number of photon packages.

  2. 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

  3. 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 investigated…

  4. 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.

  5. 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)

  6. Exchange bias of conetic thin films

    NASA Astrophysics Data System (ADS)

    Eggers, Tatiana; Kirby, Hillary; Jayathilaka, Priyanga; Campbell, Scott; Miller, Casey

    2012-02-01

    In this work, we study the exchange bias and coercivity of Ni77Fe14Cu5Mo4 (Conetic, also known as mu-metal) exchange coupled with FeMn as functions of Conetic thickness and buffer layer material. The samples studied were BL(30nm)/Conetic(9nm-30nm)/FeMn(10nm)/Ta(5nm), where BL = Cu or Ta. All samples were grown by magnetron sputtering in a deposition field of ˜150 Oe during growth to set the exchange bias axis. Room temperature hysteresis loops were measured by a magneto-optical Kerr effect magnetometer as a function of applied-field angle. For each variety of sample, the exchange bias and coercivity were inversely proportional to Conetic thickness. With Cu buffer layers grown on Si, the Heb decreased from 300 Oe to 62 Oe, and Hc decreased from 99 Oe to 9 Oe. Similar results were found when the Cu buffer layer was grown on SiOx, though the maximum coercivity was only 67 Oe. For the samples grown on Si(001)/Ta(5nm), the exchange bias decreased from 80 Oe to 14 Oe, while the coercivity increases only slightly from 2 Oe to 10 Oe. These results indicate a trade-off between preserving the softness of the ferromagnet and having a large exchange, which may be useful for tuning the performance of low-field sensing materials

  7. 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

  8. 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

  9. 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…

  10. 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.

  11. Nonlinear vs. linear biasing in Trp-cage folding simulations

    NASA Astrophysics Data System (ADS)

    Spiwok, Vojtěch; Oborský, Pavel; Pazúriková, Jana; Křenek, Aleš; Králová, Blanka

    2015-03-01

    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.

  12. Magnification bias in galactic microlensing searches

    NASA Technical Reports Server (NTRS)

    Nemiroff, Robert J.

    1994-01-01

    It is shown that a significant amount of detectable gravitational microlensing events that could potentially be found by Massively Parallel Photometry (MAPP) project (such as the MACHO, EROS, and OGLE collaborations) will occur for stars too dim to be easily noticed individually by these projects. This is the result of a large magnification bias effect, a bias of including high-magnification events in any flux-limited sample. The probablility of detecting these events may be as high as 2.3 times the lensing probability of stars currently being monitored by MAPP collaborations.

  13. 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.

  14. 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.

  15. Oxygen configurations in silica

    SciTech Connect

    Chelikowsky, James R.; Chadi, D. J.; Binggeli, N.

    2000-07-15

    We propose a transition state for oxygen in silica. This state is produced by the insertion of an oxygen molecule into the Si-O-Si bond, i.e., it consists of producing a Si-O-O-O-Si bond. This state allows molecular oxygen diffusion in silica without breaking the molecular O{sub 2} bond and it is energetically more stable than a peroxy configuration. This configuration may allow for exchange of molecular oxygen with the oxygen in the silica framework. (c) 2000 The American Physical Society.

  16. 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…

  17. Negativity bias and basic values.

    PubMed

    Schwartz, Shalom H

    2014-06-01

    Basic values explain more variance in political attitudes and preferences than other personality and sociodemographic variables. The values most relevant to the political domain are those likely to reflect the degree of negativity bias. Value conflicts that represent negativity bias clarify differences between what worries conservatives and liberals and suggest that relations between ideology and negativity bias are linear. PMID:24970450

  18. Assessing Bias in Search Engines.

    ERIC Educational Resources Information Center

    Mowshowitz, Abbe; Kawaguchi, Akira

    2002-01-01

    Addresses the measurement of bias in search engines on the Web, defining bias as the balance and representation of items in a collection retrieved from a database for a set of queries. Assesses bias by measuring the deviation from the ideal of the distribution produced by a particular search engine. (Author/LRW)

  19. Test Bias and the Elimination of Racism

    ERIC Educational Resources Information Center

    Sedlacek, William E.

    1977-01-01

    Three types of test bias are discussed: content bias, atmosphere bias, and use bias. Use bias is considered the most important. Tests reflect the bias in society, and eliminating test bias means eliminating racism and sexism in society. A six-stage model to eliminate racism and sexism is presented. (Author)

  20. 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…

  1. Sonic boom configuration minimization

    NASA Technical Reports Server (NTRS)

    Sohn, Robert A.

    1992-01-01

    The topics covered include the following: the sonic boom 'big picture'; current low boom technology; Mach number impact on gross weight; equal loudness equivalent areas; performance and sizing results; potential configuration modifications; equivalent area matching; and impact of nose bluntness on aerodynamic characteristics.

  2. Space Station Final Configuration

    NASA Technical Reports Server (NTRS)

    1994-01-01

    An artist's conception of what the final configuration of the International Space Station (ISS) will look like when it is fully built and deployed. The ISS is a multidisciplinary laboratory, technology test bed, and observatory that will provide an unprecedented undertaking in scientific, technological, and international experimentation.

  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. Attentional Bias towards Positive Emotion Predicts Stress Resilience.

    PubMed

    Thoern, Hanna A; Grueschow, Marcus; Ehlert, Ulrike; Ruff, Christian C; Kleim, Birgit

    2016-01-01

    There is extensive evidence for an association between an attentional bias towards emotionally negative stimuli and vulnerability to stress-related psychopathology. Less is known about whether selective attention towards emotionally positive stimuli relates to mental health and stress resilience. The current study used a modified Dot Probe task to investigate if individual differences in attentional biases towards either happy or angry emotional stimuli, or an interaction between these biases, are related to self-reported trait stress resilience. In a nonclinical sample (N = 43), we indexed attentional biases as individual differences in reaction time for stimuli preceded by either happy or angry (compared to neutral) face stimuli. Participants with greater attentional bias towards happy faces (but not angry faces) reported higher trait resilience. However, an attentional bias towards angry stimuli moderated this effect: The attentional bias towards happy faces was only predictive for resilience in those individuals who also endorsed an attentional bias towards angry stimuli. An attentional bias towards positive emotional stimuli may thus be a protective factor contributing to stress resilience, specifically in those individuals who also endorse an attentional bias towards negative emotional stimuli. Our findings therefore suggest a novel target for prevention and treatment interventions addressing stress-related psychopathology. PMID:27008475

  5. Attentional Bias towards Positive Emotion Predicts Stress Resilience

    PubMed Central

    Ehlert, Ulrike; Ruff, Christian C.; Kleim, Birgit

    2016-01-01

    There is extensive evidence for an association between an attentional bias towards emotionally negative stimuli and vulnerability to stress-related psychopathology. Less is known about whether selective attention towards emotionally positive stimuli relates to mental health and stress resilience. The current study used a modified Dot Probe task to investigate if individual differences in attentional biases towards either happy or angry emotional stimuli, or an interaction between these biases, are related to self-reported trait stress resilience. In a nonclinical sample (N = 43), we indexed attentional biases as individual differences in reaction time for stimuli preceded by either happy or angry (compared to neutral) face stimuli. Participants with greater attentional bias towards happy faces (but not angry faces) reported higher trait resilience. However, an attentional bias towards angry stimuli moderated this effect: The attentional bias towards happy faces was only predictive for resilience in those individuals who also endorsed an attentional bias towards angry stimuli. An attentional bias towards positive emotional stimuli may thus be a protective factor contributing to stress resilience, specifically in those individuals who also endorse an attentional bias towards negative emotional stimuli. Our findings therefore suggest a novel target for prevention and treatment interventions addressing stress-related psychopathology. PMID:27008475

  6. Assessment of risk of bias in translational science

    PubMed Central

    2013-01-01

    Risk of bias in translational medicine may take one of three forms: A. a systematic error of methodology as it pertains to measurement or sampling (e.g., selection bias), B. a systematic defect of design that leads to estimates of experimental and control groups, and of effect sizes that substantially deviate from true values (e.g., information bias), and C. a systematic distortion of the analytical process, which results in a misrepresentation of the data with consequential errors of inference (e.g., inferential bias). Risk of bias can seriously adulterate the internal and the external validity of a clinical study, and, unless it is identified and systematically evaluated, can seriously hamper the process of comparative effectiveness and efficacy research and analysis for practice. The Cochrane Group and the Agency for Healthcare Research and Quality have independently developed instruments for assessing the meta-construct of risk of bias. The present article begins to discuss this dialectic. PMID:23927081

  7. First principle simulations of a bias-dependent electrochemical cell

    NASA Astrophysics Data System (ADS)

    Pedroza, Luana; Brandimarte, Pedro; Fernandez-Serra, Marivi; Rocha, Alexandre R.

    Understanding the local structure of water molecules at the interfaces of metallic electrodes is a key problem in many electrochemical problems. Notably the system is under an external potential bias, which makes the task of simulating this setup difficult. To correctly compute the effect of an external bias potential applied to electrodes, we combine density functional theory and non-equilibrium Green's functions methods, with and without van der Waals interactions. In this work, we apply this methodology to study the electronic properties and forces of water molecules at the interface of different metallic electrodes. We find that the water molecule is sensitive to the sign and magnitude of the applied bias. We also show that it changes the position and orientation of the most stable configuration indicating that the external bias plays an important role in the structural properties of the interface. The authors thank FAPESP and CNPq for financial support.

  8. Is there gender bias in nursing research?

    PubMed

    Polit, Denise F; Beck, Cheryl Tatano

    2008-10-01

    Using data from a consecutive sample of 259 studies published in four leading nursing research journals in 2005-2006, we examined whether nurse researchers favor females as study participants. On average, 75.3% of study participants were female, and 38% of studies had all-female samples. The bias favoring female participants was statistically significant and persistent. The bias was observed regardless of funding source, methodological features, and other participant and researcher characteristics, with one exception: studies that had male investigators had more sex-balanced samples. When designing studies, nurse researchers need to pay close attention to who will benefit from their research and to whether they are leaving out a specific group about which there is a gap in knowledge. PMID:18324681

  9. Review of Bias Field Operation on SSPX

    NASA Astrophysics Data System (ADS)

    Wood, R. D.

    2005-10-01

    We have carried out experiments to explore how different vacuum magnetic-field configurations affect plasma performance on SSPX. Six independently controllable magnetic field coils and power supplies can be programmed to obtain a wide range of field line configurations: those with vacuum magnetic field lines passing parallel to the side walls of the SSPX chamber and those with diverging fields passing through the side walls of the chamber. The new coils have greatly expanded the density range over which good spheromak plasmas are observed. This results from the ability to form, using the bias coils, a Penning discharge so that spheromak formation can be obtained at lower input gas pressure. In addition, spheromak theory suggests an increase in field amplification could be expected with magnetic field lines parallel to the chamber walls. We observed about a 20% increase in field amplification suggesting that current flow during formation and the resultant MHD stability play an important role in magnetic field build up. Energy confinement and magnetic field generation during operation with the bias coils will be presented. This work performed under the auspices of the USDOE and the University of California Lawrence Livermore National Laboratory under Contract No. W-7405-ENG-48

  10. Evaluating solutions to sponsorship bias.

    PubMed

    Doucet, M; Sismondo, S

    2008-08-01

    More than 40 primary studies, and three recent systematic reviews and meta-analyses, have shown a clear association between pharmaceutical industry funding of clinical trials and pro-industry results. Industry sponsorship biases published scientific research in favour of the sponsors, a result of the strong interest commercial sponsors have in obtaining favourable results. Three proposed remedies to this problem are widely agreed upon among those concerned with the level of sponsorship bias: financial disclosure, reporting standards and trial registries. This paper argues that all of these remedies either fail to address the mechanisms by which pharmaceutical companies' sponsorship leads to biased results-design bias, multiple trials with predictable outcomes, fraud, rhetorical effects and publication bias-or else only inadequately address those mechanisms. As a result, the policies normally proposed for dealing with sponsorship bias are unable to eliminate it. Only completely separating public clinical research from pharmaceutical industry funding can eliminate sponsorship bias. PMID:18667655