Sample records for importance sampling method

  1. Some connections between importance sampling and enhanced sampling methods in molecular dynamics

    NASA Astrophysics Data System (ADS)

    Lie, H. C.; Quer, J.

    2017-11-01

    In molecular dynamics, enhanced sampling methods enable the collection of better statistics of rare events from a reference or target distribution. We show that a large class of these methods is based on the idea of importance sampling from mathematical statistics. We illustrate this connection by comparing the Hartmann-Schütte method for rare event simulation (J. Stat. Mech. Theor. Exp. 2012, P11004) and the Valsson-Parrinello method of variationally enhanced sampling [Phys. Rev. Lett. 113, 090601 (2014)]. We use this connection in order to discuss how recent results from the Monte Carlo methods literature can guide the development of enhanced sampling methods.

  2. Some connections between importance sampling and enhanced sampling methods in molecular dynamics.

    PubMed

    Lie, H C; Quer, J

    2017-11-21

    In molecular dynamics, enhanced sampling methods enable the collection of better statistics of rare events from a reference or target distribution. We show that a large class of these methods is based on the idea of importance sampling from mathematical statistics. We illustrate this connection by comparing the Hartmann-Schütte method for rare event simulation (J. Stat. Mech. Theor. Exp. 2012, P11004) and the Valsson-Parrinello method of variationally enhanced sampling [Phys. Rev. Lett. 113, 090601 (2014)]. We use this connection in order to discuss how recent results from the Monte Carlo methods literature can guide the development of enhanced sampling methods.

  3. A flexible importance sampling method for integrating subgrid processes

    DOE PAGES

    Raut, E. K.; Larson, V. E.

    2016-01-29

    Numerical models of weather and climate need to compute grid-box-averaged rates of physical processes such as microphysics. These averages are computed by integrating subgrid variability over a grid box. For this reason, an important aspect of atmospheric modeling is spatial integration over subgrid scales. The needed integrals can be estimated by Monte Carlo integration. Monte Carlo integration is simple and general but requires many evaluations of the physical process rate. To reduce the number of function evaluations, this paper describes a new, flexible method of importance sampling. It divides the domain of integration into eight categories, such as the portion that containsmore » both precipitation and cloud, or the portion that contains precipitation but no cloud. It then allows the modeler to prescribe the density of sample points within each of the eight categories. The new method is incorporated into the Subgrid Importance Latin Hypercube Sampler (SILHS). Here, the resulting method is tested on drizzling cumulus and stratocumulus cases. In the cumulus case, the sampling error can be considerably reduced by drawing more sample points from the region of rain evaporation.« less

  4. State-dependent biasing method for importance sampling in the weighted stochastic simulation algorithm.

    PubMed

    Roh, Min K; Gillespie, Dan T; Petzold, Linda R

    2010-11-07

    The weighted stochastic simulation algorithm (wSSA) was developed by Kuwahara and Mura [J. Chem. Phys. 129, 165101 (2008)] to efficiently estimate the probabilities of rare events in discrete stochastic systems. The wSSA uses importance sampling to enhance the statistical accuracy in the estimation of the probability of the rare event. The original algorithm biases the reaction selection step with a fixed importance sampling parameter. In this paper, we introduce a novel method where the biasing parameter is state-dependent. The new method features improved accuracy, efficiency, and robustness.

  5. Importance sampling variance reduction for the Fokker–Planck rarefied gas particle method

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Collyer, B.S., E-mail: benjamin.collyer@gmail.com; London Mathematical Laboratory, 14 Buckingham Street, London WC2N 6DF; Connaughton, C.

    The Fokker–Planck approximation to the Boltzmann equation, solved numerically by stochastic particle schemes, is used to provide estimates for rarefied gas flows. This paper presents a variance reduction technique for a stochastic particle method that is able to greatly reduce the uncertainty of the estimated flow fields when the characteristic speed of the flow is small in comparison to the thermal velocity of the gas. The method relies on importance sampling, requiring minimal changes to the basic stochastic particle scheme. We test the importance sampling scheme on a homogeneous relaxation, planar Couette flow and a lid-driven-cavity flow, and find thatmore » our method is able to greatly reduce the noise of estimated quantities. Significantly, we find that as the characteristic speed of the flow decreases, the variance of the noisy estimators becomes independent of the characteristic speed.« less

  6. Comparison of estimates of hardwood bole volume using importance sampling, the centroid method, and some taper equations

    Treesearch

    Harry V., Jr. Wiant; Michael L. Spangler; John E. Baumgras

    2002-01-01

    Various taper systems and the centroid method were compared to unbiased volume estimates made by importance sampling for 720 hardwood trees selected throughout the state of West Virginia. Only the centroid method consistently gave volumes estimates that did not differ significantly from those made by importance sampling, although some taper equations did well for most...

  7. Annealed importance sampling with constant cooling rate

    NASA Astrophysics Data System (ADS)

    Giovannelli, Edoardo; Cardini, Gianni; Gellini, Cristina; Pietraperzia, Giangaetano; Chelli, Riccardo

    2015-02-01

    Annealed importance sampling is a simulation method devised by Neal [Stat. Comput. 11, 125 (2001)] to assign weights to configurations generated by simulated annealing trajectories. In particular, the equilibrium average of a generic physical quantity can be computed by a weighted average exploiting weights and estimates of this quantity associated to the final configurations of the annealed trajectories. Here, we review annealed importance sampling from the perspective of nonequilibrium path-ensemble averages [G. E. Crooks, Phys. Rev. E 61, 2361 (2000)]. The equivalence of Neal's and Crooks' treatments highlights the generality of the method, which goes beyond the mere thermal-based protocols. Furthermore, we show that a temperature schedule based on a constant cooling rate outperforms stepwise cooling schedules and that, for a given elapsed computer time, performances of annealed importance sampling are, in general, improved by increasing the number of intermediate temperatures.

  8. Nuclear Ensemble Approach with Importance Sampling.

    PubMed

    Kossoski, Fábris; Barbatti, Mario

    2018-06-12

    We show that the importance sampling technique can effectively augment the range of problems where the nuclear ensemble approach can be applied. A sampling probability distribution function initially determines the collection of initial conditions for which calculations are performed, as usual. Then, results for a distinct target distribution are computed by introducing compensating importance sampling weights for each sampled point. This mapping between the two probability distributions can be performed whenever they are both explicitly constructed. Perhaps most notably, this procedure allows for the computation of temperature dependent observables. As a test case, we investigated the UV absorption spectra of phenol, which has been shown to have a marked temperature dependence. Application of the proposed technique to a range that covers 500 K provides results that converge to those obtained with conventional sampling. We further show that an overall improved rate of convergence is obtained when sampling is performed at intermediate temperatures. The comparison between calculated and the available measured cross sections is very satisfactory, as the main features of the spectra are correctly reproduced. As a second test case, one of Tully's classical models was revisited, and we show that the computation of dynamical observables also profits from the importance sampling technique. In summary, the strategy developed here can be employed to assess the role of temperature for any property calculated within the nuclear ensemble method, with the same computational cost as doing so for a single temperature.

  9. Probabilistic inference using linear Gaussian importance sampling for hybrid Bayesian networks

    NASA Astrophysics Data System (ADS)

    Sun, Wei; Chang, K. C.

    2005-05-01

    Probabilistic inference for Bayesian networks is in general NP-hard using either exact algorithms or approximate methods. However, for very complex networks, only the approximate methods such as stochastic sampling could be used to provide a solution given any time constraint. There are several simulation methods currently available. They include logic sampling (the first proposed stochastic method for Bayesian networks, the likelihood weighting algorithm) the most commonly used simulation method because of its simplicity and efficiency, the Markov blanket scoring method, and the importance sampling algorithm. In this paper, we first briefly review and compare these available simulation methods, then we propose an improved importance sampling algorithm called linear Gaussian importance sampling algorithm for general hybrid model (LGIS). LGIS is aimed for hybrid Bayesian networks consisting of both discrete and continuous random variables with arbitrary distributions. It uses linear function and Gaussian additive noise to approximate the true conditional probability distribution for continuous variable given both its parents and evidence in a Bayesian network. One of the most important features of the newly developed method is that it can adaptively learn the optimal important function from the previous samples. We test the inference performance of LGIS using a 16-node linear Gaussian model and a 6-node general hybrid model. The performance comparison with other well-known methods such as Junction tree (JT) and likelihood weighting (LW) shows that LGIS-GHM is very promising.

  10. Importance Sampling Variance Reduction in GRESS ATMOSIM

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wakeford, Daniel Tyler

    This document is intended to introduce the importance sampling method of variance reduction to a Geant4 user for application to neutral particle Monte Carlo transport through the atmosphere, as implemented in GRESS ATMOSIM.

  11. Honest Importance Sampling with Multiple Markov Chains

    PubMed Central

    Tan, Aixin; Doss, Hani; Hobert, James P.

    2017-01-01

    Importance sampling is a classical Monte Carlo technique in which a random sample from one probability density, π1, is used to estimate an expectation with respect to another, π. The importance sampling estimator is strongly consistent and, as long as two simple moment conditions are satisfied, it obeys a central limit theorem (CLT). Moreover, there is a simple consistent estimator for the asymptotic variance in the CLT, which makes for routine computation of standard errors. Importance sampling can also be used in the Markov chain Monte Carlo (MCMC) context. Indeed, if the random sample from π1 is replaced by a Harris ergodic Markov chain with invariant density π1, then the resulting estimator remains strongly consistent. There is a price to be paid however, as the computation of standard errors becomes more complicated. First, the two simple moment conditions that guarantee a CLT in the iid case are not enough in the MCMC context. Second, even when a CLT does hold, the asymptotic variance has a complex form and is difficult to estimate consistently. In this paper, we explain how to use regenerative simulation to overcome these problems. Actually, we consider a more general set up, where we assume that Markov chain samples from several probability densities, π1, …, πk, are available. We construct multiple-chain importance sampling estimators for which we obtain a CLT based on regeneration. We show that if the Markov chains converge to their respective target distributions at a geometric rate, then under moment conditions similar to those required in the iid case, the MCMC-based importance sampling estimator obeys a CLT. Furthermore, because the CLT is based on a regenerative process, there is a simple consistent estimator of the asymptotic variance. We illustrate the method with two applications in Bayesian sensitivity analysis. The first concerns one-way random effects models under different priors. The second involves Bayesian variable selection in

  12. Honest Importance Sampling with Multiple Markov Chains.

    PubMed

    Tan, Aixin; Doss, Hani; Hobert, James P

    2015-01-01

    Importance sampling is a classical Monte Carlo technique in which a random sample from one probability density, π 1 , is used to estimate an expectation with respect to another, π . The importance sampling estimator is strongly consistent and, as long as two simple moment conditions are satisfied, it obeys a central limit theorem (CLT). Moreover, there is a simple consistent estimator for the asymptotic variance in the CLT, which makes for routine computation of standard errors. Importance sampling can also be used in the Markov chain Monte Carlo (MCMC) context. Indeed, if the random sample from π 1 is replaced by a Harris ergodic Markov chain with invariant density π 1 , then the resulting estimator remains strongly consistent. There is a price to be paid however, as the computation of standard errors becomes more complicated. First, the two simple moment conditions that guarantee a CLT in the iid case are not enough in the MCMC context. Second, even when a CLT does hold, the asymptotic variance has a complex form and is difficult to estimate consistently. In this paper, we explain how to use regenerative simulation to overcome these problems. Actually, we consider a more general set up, where we assume that Markov chain samples from several probability densities, π 1 , …, π k , are available. We construct multiple-chain importance sampling estimators for which we obtain a CLT based on regeneration. We show that if the Markov chains converge to their respective target distributions at a geometric rate, then under moment conditions similar to those required in the iid case, the MCMC-based importance sampling estimator obeys a CLT. Furthermore, because the CLT is based on a regenerative process, there is a simple consistent estimator of the asymptotic variance. We illustrate the method with two applications in Bayesian sensitivity analysis. The first concerns one-way random effects models under different priors. The second involves Bayesian variable

  13. Adaptive Importance Sampling for Control and Inference

    NASA Astrophysics Data System (ADS)

    Kappen, H. J.; Ruiz, H. C.

    2016-03-01

    Path integral (PI) control problems are a restricted class of non-linear control problems that can be solved formally as a Feynman-Kac PI and can be estimated using Monte Carlo sampling. In this contribution we review PI control theory in the finite horizon case. We subsequently focus on the problem how to compute and represent control solutions. We review the most commonly used methods in robotics and control. Within the PI theory, the question of how to compute becomes the question of importance sampling. Efficient importance samplers are state feedback controllers and the use of these requires an efficient representation. Learning and representing effective state-feedback controllers for non-linear stochastic control problems is a very challenging, and largely unsolved, problem. We show how to learn and represent such controllers using ideas from the cross entropy method. We derive a gradient descent method that allows to learn feed-back controllers using an arbitrary parametrisation. We refer to this method as the path integral cross entropy method or PICE. We illustrate this method for some simple examples. The PI control methods can be used to estimate the posterior distribution in latent state models. In neuroscience these problems arise when estimating connectivity from neural recording data using EM. We demonstrate the PI control method as an accurate alternative to particle filtering.

  14. An efficient reliability algorithm for locating design point using the combination of importance sampling concepts and response surface method

    NASA Astrophysics Data System (ADS)

    Shayanfar, Mohsen Ali; Barkhordari, Mohammad Ali; Roudak, Mohammad Amin

    2017-06-01

    Monte Carlo simulation (MCS) is a useful tool for computation of probability of failure in reliability analysis. However, the large number of required random samples makes it time-consuming. Response surface method (RSM) is another common method in reliability analysis. Although RSM is widely used for its simplicity, it cannot be trusted in highly nonlinear problems due to its linear nature. In this paper, a new efficient algorithm, employing the combination of importance sampling, as a class of MCS, and RSM is proposed. In the proposed algorithm, analysis starts with importance sampling concepts and using a represented two-step updating rule of design point. This part finishes after a small number of samples are generated. Then RSM starts to work using Bucher experimental design, with the last design point and a represented effective length as the center point and radius of Bucher's approach, respectively. Through illustrative numerical examples, simplicity and efficiency of the proposed algorithm and the effectiveness of the represented rules are shown.

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

    PubMed Central

    Cao, Youfang; Liang, Jie

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Cao, Youfang; Liang, Jie

    2013-07-01

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

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

    PubMed

    Cao, Youfang; Liang, Jie

    2013-07-14

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

  18. Screen Space Ambient Occlusion Based Multiple Importance Sampling for Real-Time Rendering

    NASA Astrophysics Data System (ADS)

    Zerari, Abd El Mouméne; Babahenini, Mohamed Chaouki

    2018-03-01

    We propose a new approximation technique for accelerating the Global Illumination algorithm for real-time rendering. The proposed approach is based on the Screen-Space Ambient Occlusion (SSAO) method, which approximates the global illumination for large, fully dynamic scenes at interactive frame rates. Current algorithms that are based on the SSAO method suffer from difficulties due to the large number of samples that are required. In this paper, we propose an improvement to the SSAO technique by integrating it with a Multiple Importance Sampling technique that combines a stratified sampling method with an importance sampling method, with the objective of reducing the number of samples. Experimental evaluation demonstrates that our technique can produce high-quality images in real time and is significantly faster than traditional techniques.

  19. Perpendicular distance sampling: an alternative method for sampling downed coarse woody debris

    Treesearch

    Michael S. Williams; Jeffrey H. Gove

    2003-01-01

    Coarse woody debris (CWD) plays an important role in many forest ecosystem processes. In recent years, a number of new methods have been proposed to sample CWD. These methods select individual logs into the sample using some form of unequal probability sampling. One concern with most of these methods is the difficulty in estimating the volume of each log. A new method...

  20. Convergence and Efficiency of Adaptive Importance Sampling Techniques with Partial Biasing

    NASA Astrophysics Data System (ADS)

    Fort, G.; Jourdain, B.; Lelièvre, T.; Stoltz, G.

    2018-04-01

    We propose a new Monte Carlo method to efficiently sample a multimodal distribution (known up to a normalization constant). We consider a generalization of the discrete-time Self Healing Umbrella Sampling method, which can also be seen as a generalization of well-tempered metadynamics. The dynamics is based on an adaptive importance technique. The importance function relies on the weights (namely the relative probabilities) of disjoint sets which form a partition of the space. These weights are unknown but are learnt on the fly yielding an adaptive algorithm. In the context of computational statistical physics, the logarithm of these weights is, up to an additive constant, the free-energy, and the discrete valued function defining the partition is called the collective variable. The algorithm falls into the general class of Wang-Landau type methods, and is a generalization of the original Self Healing Umbrella Sampling method in two ways: (i) the updating strategy leads to a larger penalization strength of already visited sets in order to escape more quickly from metastable states, and (ii) the target distribution is biased using only a fraction of the free-energy, in order to increase the effective sample size and reduce the variance of importance sampling estimators. We prove the convergence of the algorithm and analyze numerically its efficiency on a toy example.

  1. A new method for estimating the demographic history from DNA sequences: an importance sampling approach

    PubMed Central

    Ait Kaci Azzou, Sadoune; Larribe, Fabrice; Froda, Sorana

    2015-01-01

    The effective population size over time (demographic history) can be retraced from a sample of contemporary DNA sequences. In this paper, we propose a novel methodology based on importance sampling (IS) for exploring such demographic histories. Our starting point is the generalized skyline plot with the main difference being that our procedure, skywis plot, uses a large number of genealogies. The information provided by these genealogies is combined according to the IS weights. Thus, we compute a weighted average of the effective population sizes on specific time intervals (epochs), where the genealogies that agree more with the data are given more weight. We illustrate by a simulation study that the skywis plot correctly reconstructs the recent demographic history under the scenarios most commonly considered in the literature. In particular, our method can capture a change point in the effective population size, and its overall performance is comparable with the one of the bayesian skyline plot. We also introduce the case of serially sampled sequences and illustrate that it is possible to improve the performance of the skywis plot in the case of an exponential expansion of the effective population size. PMID:26300910

  2. Time-dependent importance sampling in semiclassical initial value representation calculations for time correlation functions.

    PubMed

    Tao, Guohua; Miller, William H

    2011-07-14

    An efficient time-dependent importance sampling method is developed for the Monte Carlo calculation of time correlation functions via the initial value representation (IVR) of semiclassical (SC) theory. A prefactor-free time-dependent sampling function weights the importance of a trajectory based on the magnitude of its contribution to the time correlation function, and global trial moves are used to facilitate the efficient sampling the phase space of initial conditions. The method can be generally applied to sampling rare events efficiently while avoiding being trapped in a local region of the phase space. Results presented in the paper for two system-bath models demonstrate the efficiency of this new importance sampling method for full SC-IVR calculations.

  3. Importance sampling studies of helium using the Feynman-Kac path integral method

    NASA Astrophysics Data System (ADS)

    Datta, S.; Rejcek, J. M.

    2018-05-01

    In the Feynman-Kac path integral approach the eigenvalues of a quantum system can be computed using Wiener measure which uses Brownian particle motion. In our previous work on such systems we have observed that the Wiener process numerically converges slowly for dimensions greater than two because almost all trajectories will escape to infinity. One can speed up this process by using a generalized Feynman-Kac (GFK) method, in which the new measure associated with the trial function is stationary, so that the convergence rate becomes much faster. We thus achieve an example of "importance sampling" and, in the present work, we apply it to the Feynman-Kac (FK) path integrals for the ground and first few excited-state energies for He to speed up the convergence rate. We calculate the path integrals using space averaging rather than the time averaging as done in the past. The best previous calculations from variational computations report precisions of 10-16 Hartrees, whereas in most cases our path integral results obtained for the ground and first excited states of He are lower than these results by about 10-6 Hartrees or more.

  4. Sampling High-Altitude and Stratified Mating Flights of Red Imported Fire Ant

    USDA-ARS?s Scientific Manuscript database

    With the exception of an airplane equipped with nets, no method has been developed that successfully samples red imported fire ant, Solenopsis invicta Buren, sexuals in mating/dispersal flights throughout their potential altitudinal trajectories. We developed and tested a method for sampling queens ...

  5. An improved sampling method of complex network

    NASA Astrophysics Data System (ADS)

    Gao, Qi; Ding, Xintong; Pan, Feng; Li, Weixing

    2014-12-01

    Sampling subnet is an important topic of complex network research. Sampling methods influence the structure and characteristics of subnet. Random multiple snowball with Cohen (RMSC) process sampling which combines the advantages of random sampling and snowball sampling is proposed in this paper. It has the ability to explore global information and discover the local structure at the same time. The experiments indicate that this novel sampling method could keep the similarity between sampling subnet and original network on degree distribution, connectivity rate and average shortest path. This method is applicable to the situation where the prior knowledge about degree distribution of original network is not sufficient.

  6. Annealed Importance Sampling Reversible Jump MCMC algorithms

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Karagiannis, Georgios; Andrieu, Christophe

    2013-03-20

    It will soon be 20 years since reversible jump Markov chain Monte Carlo (RJ-MCMC) algorithms have been proposed. They have significantly extended the scope of Markov chain Monte Carlo simulation methods, offering the promise to be able to routinely tackle transdimensional sampling problems, as encountered in Bayesian model selection problems for example, in a principled and flexible fashion. Their practical efficient implementation, however, still remains a challenge. A particular difficulty encountered in practice is in the choice of the dimension matching variables (both their nature and their distribution) and the reversible transformations which allow one to define the one-to-one mappingsmore » underpinning the design of these algorithms. Indeed, even seemingly sensible choices can lead to algorithms with very poor performance. The focus of this paper is the development and performance evaluation of a method, annealed importance sampling RJ-MCMC (aisRJ), which addresses this problem by mitigating the sensitivity of RJ-MCMC algorithms to the aforementioned poor design. As we shall see the algorithm can be understood as being an “exact approximation” of an idealized MCMC algorithm that would sample from the model probabilities directly in a model selection set-up. Such an idealized algorithm may have good theoretical convergence properties, but typically cannot be implemented, and our algorithms can approximate the performance of such idealized algorithms to an arbitrary degree while not introducing any bias for any degree of approximation. Our approach combines the dimension matching ideas of RJ-MCMC with annealed importance sampling and its Markov chain Monte Carlo implementation. We illustrate the performance of the algorithm with numerical simulations which indicate that, although the approach may at first appear computationally involved, it is in fact competitive.« less

  7. A Comparison of EPI Sampling, Probability Sampling, and Compact Segment Sampling Methods for Micro and Small Enterprises

    PubMed Central

    Chao, Li-Wei; Szrek, Helena; Peltzer, Karl; Ramlagan, Shandir; Fleming, Peter; Leite, Rui; Magerman, Jesswill; Ngwenya, Godfrey B.; Pereira, Nuno Sousa; Behrman, Jere

    2011-01-01

    Finding an efficient method for sampling micro- and small-enterprises (MSEs) for research and statistical reporting purposes is a challenge in developing countries, where registries of MSEs are often nonexistent or outdated. This lack of a sampling frame creates an obstacle in finding a representative sample of MSEs. This study uses computer simulations to draw samples from a census of businesses and non-businesses in the Tshwane Municipality of South Africa, using three different sampling methods: the traditional probability sampling method, the compact segment sampling method, and the World Health Organization’s Expanded Programme on Immunization (EPI) sampling method. Three mechanisms by which the methods could differ are tested, the proximity selection of respondents, the at-home selection of respondents, and the use of inaccurate probability weights. The results highlight the importance of revisits and accurate probability weights, but the lesser effect of proximity selection on the samples’ statistical properties. PMID:22582004

  8. Sampling Methods in Cardiovascular Nursing Research: An Overview.

    PubMed

    Kandola, Damanpreet; Banner, Davina; O'Keefe-McCarthy, Sheila; Jassal, Debbie

    2014-01-01

    Cardiovascular nursing research covers a wide array of topics from health services to psychosocial patient experiences. The selection of specific participant samples is an important part of the research design and process. The sampling strategy employed is of utmost importance to ensure that a representative sample of participants is chosen. There are two main categories of sampling methods: probability and non-probability. Probability sampling is the random selection of elements from the population, where each element of the population has an equal and independent chance of being included in the sample. There are five main types of probability sampling including simple random sampling, systematic sampling, stratified sampling, cluster sampling, and multi-stage sampling. Non-probability sampling methods are those in which elements are chosen through non-random methods for inclusion into the research study and include convenience sampling, purposive sampling, and snowball sampling. Each approach offers distinct advantages and disadvantages and must be considered critically. In this research column, we provide an introduction to these key sampling techniques and draw on examples from the cardiovascular research. Understanding the differences in sampling techniques may aid nurses in effective appraisal of research literature and provide a reference pointfor nurses who engage in cardiovascular research.

  9. Fast Bayesian experimental design: Laplace-based importance sampling for the expected information gain

    NASA Astrophysics Data System (ADS)

    Beck, Joakim; Dia, Ben Mansour; Espath, Luis F. R.; Long, Quan; Tempone, Raúl

    2018-06-01

    In calculating expected information gain in optimal Bayesian experimental design, the computation of the inner loop in the classical double-loop Monte Carlo requires a large number of samples and suffers from underflow if the number of samples is small. These drawbacks can be avoided by using an importance sampling approach. We present a computationally efficient method for optimal Bayesian experimental design that introduces importance sampling based on the Laplace method to the inner loop. We derive the optimal values for the method parameters in which the average computational cost is minimized according to the desired error tolerance. We use three numerical examples to demonstrate the computational efficiency of our method compared with the classical double-loop Monte Carlo, and a more recent single-loop Monte Carlo method that uses the Laplace method as an approximation of the return value of the inner loop. The first example is a scalar problem that is linear in the uncertain parameter. The second example is a nonlinear scalar problem. The third example deals with the optimal sensor placement for an electrical impedance tomography experiment to recover the fiber orientation in laminate composites.

  10. Comparison of Two Methods for the Isolation of Salmonellae From Imported Foods

    PubMed Central

    Taylor, Welton I.; Hobbs, Betty C.; Smith, Muriel E.

    1964-01-01

    Two methods for the detection of salmonellae in foods were compared in 179 imported meat and egg samples. The number of positive samples and replications, and the number of strains and kinds of serotypes were statistically comparable by both the direct enrichment method of the Food Hygiene Laboratory in England, and the pre-enrichment method devised for processed foods in the United States. Boneless frozen beef, veal, and horsemeat imported from five countries for consumption in England were found to have salmonellae present in 48 of 116 (41%) samples. Dried egg products imported from three countries were observed to have salmonellae in 10 of 63 (16%) samples. The high incidence of salmonellae isolated from imported foods illustrated the existence of an international health hazard resulting from the continuous introduction of exogenous strains of pathogenic microorganisms on a large scale. PMID:14106941

  11. COMPARISON OF TWO METHODS FOR THE ISOLATION OF SALMONELLAE FROM IMPORTED FOODS.

    PubMed

    TAYLOR, W I; HOBBS, B C; SMITH, M E

    1964-01-01

    Two methods for the detection of salmonellae in foods were compared in 179 imported meat and egg samples. The number of positive samples and replications, and the number of strains and kinds of serotypes were statistically comparable by both the direct enrichment method of the Food Hygiene Laboratory in England, and the pre-enrichment method devised for processed foods in the United States. Boneless frozen beef, veal, and horsemeat imported from five countries for consumption in England were found to have salmonellae present in 48 of 116 (41%) samples. Dried egg products imported from three countries were observed to have salmonellae in 10 of 63 (16%) samples. The high incidence of salmonellae isolated from imported foods illustrated the existence of an international health hazard resulting from the continuous introduction of exogenous strains of pathogenic microorganisms on a large scale.

  12. A LITERATURE REVIEW OF WIPE SAMPLING METHODS ...

    EPA Pesticide Factsheets

    Wipe sampling is an important technique for the estimation of contaminant deposition in buildings, homes, or outdoor surfaces as a source of possible human exposure. Numerousmethods of wipe sampling exist, and each method has its own specification for the type of wipe, wetting solvent, and determinative step to be used, depending upon the contaminant of concern. The objective of this report is to concisely summarize the findings of a literature review that was conducted to identify the state-of-the-art wipe sampling techniques for a target list of compounds. This report describes the methods used to perform the literature review; a brief review of wipe sampling techniques in general; an analysis of physical and chemical properties of each target analyte; an analysis of wipe sampling techniques for the target analyte list; and asummary of the wipe sampling techniques for the target analyte list, including existing data gaps. In general, no overwhelming consensus can be drawn from the current literature on how to collect a wipe sample for the chemical warfare agents, organophosphate pesticides, and other toxic industrial chemicals of interest to this study. Different methods, media, and wetting solvents have been recommended and used by various groups and different studies. For many of the compounds of interest, no specific wipe sampling methodology has been established for their collection. Before a wipe sampling method (or methods) can be established for the co

  13. Sampling high-altitude and stratified mating flights of red imported fire ant.

    PubMed

    Fritz, Gary N; Fritz, Ann H; Vander Meer, Robert K

    2011-05-01

    With the exception of an airplane equipped with nets, no method has been developed that successfully samples red imported fire ant, Solenopsis invicta Buren, sexuals in mating/dispersal flights throughout their potential altitudinal trajectories. We developed and tested a method for sampling queens and males during mating flights at altitudinal intervals reaching as high as "140 m. Our trapping system uses an electric winch and a 1.2-m spindle bolted to a swiveling platform. The winch dispenses up to 183 m of Kevlar-core, nylon rope and the spindle stores 10 panels (0.9 by 4.6 m each) of nylon tulle impregnated with Tangle-Trap. The panels can be attached to the rope at various intervals and hoisted into the air by using a 3-m-diameter, helium-filled balloon. Raising or lowering all 10 panels takes approximately 15-20 min. This trap also should be useful for altitudinal sampling of other insects of medical importance.

  14. Adaptive control of theophylline therapy: importance of blood sampling times.

    PubMed

    D'Argenio, D Z; Khakmahd, K

    1983-10-01

    A two-observation protocol for estimating theophylline clearance during a constant-rate intravenous infusion is used to examine the importance of blood sampling schedules with regard to the information content of resulting concentration data. Guided by a theory for calculating maximally informative sample times, population simulations are used to assess the effect of specific sampling times on the precision of resulting clearance estimates and subsequent predictions of theophylline plasma concentrations. The simulations incorporated noise terms for intersubject variability, dosing errors, sample collection errors, and assay error. Clearance was estimated using Chiou's method, least squares, and a Bayesian estimation procedure. The results of these simulations suggest that clinically significant estimation and prediction errors may result when using the above two-point protocol for estimating theophylline clearance if the time separating the two blood samples is less than one population mean elimination half-life.

  15. 19 CFR 151.67 - Sampling by importer.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 19 Customs Duties 2 2010-04-01 2010-04-01 false Sampling by importer. 151.67 Section 151.67 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Wool and Hair § 151.67 Sampling by...

  16. Extending the solvent-free MALDI sample preparation method.

    PubMed

    Hanton, Scott D; Parees, David M

    2005-01-01

    Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is an important technique to characterize many different materials, including synthetic polymers. MALDI mass spectral data can be used to determine the polymer average molecular weights, repeat units, and end groups. One of the key issues in traditional MALDI sample preparation is making good solutions of the analyte and the matrix. Solvent-free sample preparation methods have been developed to address these issues. Previous results of solvent-free or dry prepared samples show some advantages over traditional wet sample preparation methods. Although the results of the published solvent-free sample preparation methods produced excellent mass spectra, we found the method to be very time-consuming, with significant tool cleaning, which presents a significant possibility of cross contamination. To address these issues, we developed an extension of the solvent-free method that replaces the mortar and pestle grinding with ball milling the sample in a glass vial with two small steel balls. This new method generates mass spectra with equal quality of the previous methods, but has significant advantages in productivity, eliminates cross contamination, and is applicable to liquid and soft or waxy analytes.

  17. Toward cost-efficient sampling methods

    NASA Astrophysics Data System (ADS)

    Luo, Peng; Li, Yongli; Wu, Chong; Zhang, Guijie

    2015-09-01

    The sampling method has been paid much attention in the field of complex network in general and statistical physics in particular. This paper proposes two new sampling methods based on the idea that a small part of vertices with high node degree could possess the most structure information of a complex network. The two proposed sampling methods are efficient in sampling high degree nodes so that they would be useful even if the sampling rate is low, which means cost-efficient. The first new sampling method is developed on the basis of the widely used stratified random sampling (SRS) method and the second one improves the famous snowball sampling (SBS) method. In order to demonstrate the validity and accuracy of two new sampling methods, we compare them with the existing sampling methods in three commonly used simulation networks that are scale-free network, random network, small-world network, and also in two real networks. The experimental results illustrate that the two proposed sampling methods perform much better than the existing sampling methods in terms of achieving the true network structure characteristics reflected by clustering coefficient, Bonacich centrality and average path length, especially when the sampling rate is low.

  18. Estimating cross-validatory predictive p-values with integrated importance sampling for disease mapping models.

    PubMed

    Li, Longhai; Feng, Cindy X; Qiu, Shi

    2017-06-30

    An important statistical task in disease mapping problems is to identify divergent regions with unusually high or low risk of disease. Leave-one-out cross-validatory (LOOCV) model assessment is the gold standard for estimating predictive p-values that can flag such divergent regions. However, actual LOOCV is time-consuming because one needs to rerun a Markov chain Monte Carlo analysis for each posterior distribution in which an observation is held out as a test case. This paper introduces a new method, called integrated importance sampling (iIS), for estimating LOOCV predictive p-values with only Markov chain samples drawn from the posterior based on a full data set. The key step in iIS is that we integrate away the latent variables associated the test observation with respect to their conditional distribution without reference to the actual observation. By following the general theory for importance sampling, the formula used by iIS can be proved to be equivalent to the LOOCV predictive p-value. We compare iIS and other three existing methods in the literature with two disease mapping datasets. Our empirical results show that the predictive p-values estimated with iIS are almost identical to the predictive p-values estimated with actual LOOCV and outperform those given by the existing three methods, namely, the posterior predictive checking, the ordinary importance sampling, and the ghosting method by Marshall and Spiegelhalter (2003). Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  19. Sample normalization methods in quantitative metabolomics.

    PubMed

    Wu, Yiman; Li, Liang

    2016-01-22

    To reveal metabolomic changes caused by a biological event in quantitative metabolomics, it is critical to use an analytical tool that can perform accurate and precise quantification to examine the true concentration differences of individual metabolites found in different samples. A number of steps are involved in metabolomic analysis including pre-analytical work (e.g., sample collection and storage), analytical work (e.g., sample analysis) and data analysis (e.g., feature extraction and quantification). Each one of them can influence the quantitative results significantly and thus should be performed with great care. Among them, the total sample amount or concentration of metabolites can be significantly different from one sample to another. Thus, it is critical to reduce or eliminate the effect of total sample amount variation on quantification of individual metabolites. In this review, we describe the importance of sample normalization in the analytical workflow with a focus on mass spectrometry (MS)-based platforms, discuss a number of methods recently reported in the literature and comment on their applicability in real world metabolomics applications. Sample normalization has been sometimes ignored in metabolomics, partially due to the lack of a convenient means of performing sample normalization. We show that several methods are now available and sample normalization should be performed in quantitative metabolomics where the analyzed samples have significant variations in total sample amounts. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Standard methods for sampling North American freshwater fishes

    USGS Publications Warehouse

    Bonar, Scott A.; Hubert, Wayne A.; Willis, David W.

    2009-01-01

    This important reference book provides standard sampling methods recommended by the American Fisheries Society for assessing and monitoring freshwater fish populations in North America. Methods apply to ponds, reservoirs, natural lakes, and streams and rivers containing cold and warmwater fishes. Range-wide and eco-regional averages for indices of abundance, population structure, and condition for individual species are supplied to facilitate comparisons of standard data among populations. Provides information on converting nonstandard to standard data, statistical and database procedures for analyzing and storing standard data, and methods to prevent transfer of invasive species while sampling.

  1. Consistent Adjoint Driven Importance Sampling using Space, Energy and Angle

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Peplow, Douglas E.; Mosher, Scott W; Evans, Thomas M

    2012-08-01

    For challenging radiation transport problems, hybrid methods combine the accuracy of Monte Carlo methods with the global information present in deterministic methods. One of the most successful hybrid methods is CADIS Consistent Adjoint Driven Importance Sampling. This method uses a deterministic adjoint solution to construct a biased source distribution and consistent weight windows to optimize a specific tally in a Monte Carlo calculation. The method has been implemented into transport codes using just the spatial and energy information from the deterministic adjoint and has been used in many applications to compute tallies with much higher figures-of-merit than analog calculations. CADISmore » also outperforms user-supplied importance values, which usually take long periods of user time to develop. This work extends CADIS to develop weight windows that are a function of the position, energy, and direction of the Monte Carlo particle. Two types of consistent source biasing are presented: one method that biases the source in space and energy while preserving the original directional distribution and one method that biases the source in space, energy, and direction. Seven simple example problems are presented which compare the use of the standard space/energy CADIS with the new space/energy/angle treatments.« less

  2. Importance of sample preparation for molecular diagnosis of lyme borreliosis from urine.

    PubMed

    Bergmann, A R; Schmidt, B L; Derler, A-M; Aberer, E

    2002-12-01

    Urine PCR has been used for the diagnosis of Borrelia burgdorferi infection in recent years but has been abandoned because of its low sensitivity and the irreproducibility of the results. Our study aimed to analyze technical details related to sample preparation and detection methods. Crucial for a successful urine PCR were (i) avoidance of the first morning urine sample; (ii) centrifugation at 36,000 x g; and (iii) the extraction method, with only DNAzol of the seven different extraction methods used yielding positive results with patient urine specimens. Furthermore, storage of frozen urine samples at -80 degrees C reduced the sensitivity of a positive urine PCR result obtained with samples from 72 untreated erythema migrans (EM) patients from 85% in the first 3 months to <30% after more than 3 months. Bands were detected at 276 bp on ethidium bromide-stained agarose gels after amplification by a nested PCR. The specificity of bands for 32 of 33 samples was proven by hybridization with a GEN-ETI-K-DEIA kit and for a 10 further positive amplicons by sequencing. By using all of these steps to optimize the urine PCR technique, B. burgdorferi infection could be diagnosed by using urine samples from EM patients with a sensitivity (85%) substantially better than that of serological methods (50%). This improved method could be of future importance as an additional laboratory technique for the diagnosis of unclear, unrecognized borrelia infections and diseases possibly related to Lyme borreliosis.

  3. Iterative Importance Sampling Algorithms for Parameter Estimation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Grout, Ray W; Morzfeld, Matthias; Day, Marcus S.

    In parameter estimation problems one computes a posterior distribution over uncertain parameters defined jointly by a prior distribution, a model, and noisy data. Markov chain Monte Carlo (MCMC) is often used for the numerical solution of such problems. An alternative to MCMC is importance sampling, which can exhibit near perfect scaling with the number of cores on high performance computing systems because samples are drawn independently. However, finding a suitable proposal distribution is a challenging task. Several sampling algorithms have been proposed over the past years that take an iterative approach to constructing a proposal distribution. We investigate the applicabilitymore » of such algorithms by applying them to two realistic and challenging test problems, one in subsurface flow, and one in combustion modeling. More specifically, we implement importance sampling algorithms that iterate over the mean and covariance matrix of Gaussian or multivariate t-proposal distributions. Our implementation leverages massively parallel computers, and we present strategies to initialize the iterations using 'coarse' MCMC runs or Gaussian mixture models.« less

  4. Evaluation of common methods for sampling invertebrate pollinator assemblages: net sampling out-perform pan traps.

    PubMed

    Popic, Tony J; Davila, Yvonne C; Wardle, Glenda M

    2013-01-01

    Methods for sampling ecological assemblages strive to be efficient, repeatable, and representative. Unknowingly, common methods may be limited in terms of revealing species function and so of less value for comparative studies. The global decline in pollination services has stimulated surveys of flower-visiting invertebrates, using pan traps and net sampling. We explore the relative merits of these two methods in terms of species discovery, quantifying abundance, function, and composition, and responses of species to changing floral resources. Using a spatially-nested design we sampled across a 5000 km(2) area of arid grasslands, including 432 hours of net sampling and 1296 pan trap-days, between June 2010 and July 2011. Net sampling yielded 22% more species and 30% higher abundance than pan traps, and better reflected the spatio-temporal variation of floral resources. Species composition differed significantly between methods; from 436 total species, 25% were sampled by both methods, 50% only by nets, and the remaining 25% only by pans. Apart from being less comprehensive, if pan traps do not sample flower-visitors, the link to pollination is questionable. By contrast, net sampling functionally linked species to pollination through behavioural observations of flower-visitation interaction frequency. Netted specimens are also necessary for evidence of pollen transport. Benefits of net-based sampling outweighed minor differences in overall sampling effort. As pan traps and net sampling methods are not equivalent for sampling invertebrate-flower interactions, we recommend net sampling of invertebrate pollinator assemblages, especially if datasets are intended to document declines in pollination and guide measures to retain this important ecosystem service.

  5. Evaluation of Common Methods for Sampling Invertebrate Pollinator Assemblages: Net Sampling Out-Perform Pan Traps

    PubMed Central

    Popic, Tony J.; Davila, Yvonne C.; Wardle, Glenda M.

    2013-01-01

    Methods for sampling ecological assemblages strive to be efficient, repeatable, and representative. Unknowingly, common methods may be limited in terms of revealing species function and so of less value for comparative studies. The global decline in pollination services has stimulated surveys of flower-visiting invertebrates, using pan traps and net sampling. We explore the relative merits of these two methods in terms of species discovery, quantifying abundance, function, and composition, and responses of species to changing floral resources. Using a spatially-nested design we sampled across a 5000 km2 area of arid grasslands, including 432 hours of net sampling and 1296 pan trap-days, between June 2010 and July 2011. Net sampling yielded 22% more species and 30% higher abundance than pan traps, and better reflected the spatio-temporal variation of floral resources. Species composition differed significantly between methods; from 436 total species, 25% were sampled by both methods, 50% only by nets, and the remaining 25% only by pans. Apart from being less comprehensive, if pan traps do not sample flower-visitors, the link to pollination is questionable. By contrast, net sampling functionally linked species to pollination through behavioural observations of flower-visitation interaction frequency. Netted specimens are also necessary for evidence of pollen transport. Benefits of net-based sampling outweighed minor differences in overall sampling effort. As pan traps and net sampling methods are not equivalent for sampling invertebrate-flower interactions, we recommend net sampling of invertebrate pollinator assemblages, especially if datasets are intended to document declines in pollination and guide measures to retain this important ecosystem service. PMID:23799127

  6. Rapid method to determine 226Ra in steel samples

    DOE PAGES

    Maxwell, Sherrod L.; Culligan, Brian; Hutchison, Jay B.; ...

    2017-09-22

    The rapid measurement of 226Ra in steel samples is very important in the event of a radiological emergency. 226Ra (T 1/2 = 1600 y) is a natural radionuclide present in the environment and a highly toxic alpha-emitter. Due to its long life and tendency to concentrate in bones, 226Ra ingestion or inhalation can lead to significant committed dose to individuals. A new method for the determination of 226Ra in steel samples has been developed at the Savannah River Environmental Laboratory. The new method employs a rugged acid digestion method that includes hydrofluoric acid, followed by a single precipitation step tomore » rapidly preconcentrate the radium and remove most of the dissolved steel sample matrix. Radium is then separated using a combination of cation exchange and extraction chromatography, and 226Ra is measured by alpha spectrometry. This approach has a sample preparation time of ~ 8 h for steel samples, has a very high tracer yield (> 88%), and removes interferences effectively. A 133Ba yield tracer is used so that samples can be counted immediately following the separation method, avoiding lengthy ingrowth times that are required in other methods.« less

  7. Rapid method to determine 226Ra in steel samples

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Maxwell, Sherrod L.; Culligan, Brian; Hutchison, Jay B.

    The rapid measurement of 226Ra in steel samples is very important in the event of a radiological emergency. 226Ra (T 1/2 = 1600 y) is a natural radionuclide present in the environment and a highly toxic alpha-emitter. Due to its long life and tendency to concentrate in bones, 226Ra ingestion or inhalation can lead to significant committed dose to individuals. A new method for the determination of 226Ra in steel samples has been developed at the Savannah River Environmental Laboratory. The new method employs a rugged acid digestion method that includes hydrofluoric acid, followed by a single precipitation step tomore » rapidly preconcentrate the radium and remove most of the dissolved steel sample matrix. Radium is then separated using a combination of cation exchange and extraction chromatography, and 226Ra is measured by alpha spectrometry. This approach has a sample preparation time of ~ 8 h for steel samples, has a very high tracer yield (> 88%), and removes interferences effectively. A 133Ba yield tracer is used so that samples can be counted immediately following the separation method, avoiding lengthy ingrowth times that are required in other methods.« less

  8. [Sampling methods for PM2.5 from stationary sources: a review].

    PubMed

    Jiang, Jing-Kun; Deng, Jian-Guo; Li, Zhen; Li, Xing-Hua; Duan, Lei; Hao, Ji-Ming

    2014-05-01

    The new China national ambient air quality standard has been published in 2012 and will be implemented in 2016. To meet the requirements in this new standard, monitoring and controlling PM2,,5 emission from stationary sources are very important. However, so far there is no national standard method on sampling PM2.5 from stationary sources. Different sampling methods for PM2.5 from stationary sources and relevant international standards were reviewed in this study. It includes the methods for PM2.5 sampling in flue gas and the methods for PM2.5 sampling after dilution. Both advantages and disadvantages of these sampling methods were discussed. For environmental management, the method for PM2.5 sampling in flue gas such as impactor and virtual impactor was suggested as a standard to determine filterable PM2.5. To evaluate environmental and health effects of PM2.5 from stationary sources, standard dilution method for sampling of total PM2.5 should be established.

  9. 40 CFR 80.1630 - Sampling and testing requirements for refiners, gasoline importers and producers and importers of...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... refiners, gasoline importers and producers and importers of certified ethanol denaturant. 80.1630 Section...) REGULATION OF FUELS AND FUEL ADDITIVES Gasoline Sulfur § 80.1630 Sampling and testing requirements for refiners, gasoline importers and producers and importers of certified ethanol denaturant. (a) Sample and...

  10. 40 CFR 80.1349 - Alternative sampling and testing requirements for importers who import gasoline into the United...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... requirements for importers who import gasoline into the United States by truck. 80.1349 Section 80.1349... FUELS AND FUEL ADDITIVES Gasoline Benzene Sampling, Testing and Retention Requirements § 80.1349 Alternative sampling and testing requirements for importers who import gasoline into the United States by...

  11. Annealed Importance Sampling for Neural Mass Models

    PubMed Central

    Penny, Will; Sengupta, Biswa

    2016-01-01

    Neural Mass Models provide a compact description of the dynamical activity of cell populations in neocortical regions. Moreover, models of regional activity can be connected together into networks, and inferences made about the strength of connections, using M/EEG data and Bayesian inference. To date, however, Bayesian methods have been largely restricted to the Variational Laplace (VL) algorithm which assumes that the posterior distribution is Gaussian and finds model parameters that are only locally optimal. This paper explores the use of Annealed Importance Sampling (AIS) to address these restrictions. We implement AIS using proposals derived from Langevin Monte Carlo (LMC) which uses local gradient and curvature information for efficient exploration of parameter space. In terms of the estimation of Bayes factors, VL and AIS agree about which model is best but report different degrees of belief. Additionally, AIS finds better model parameters and we find evidence of non-Gaussianity in their posterior distribution. PMID:26942606

  12. Comparability of river suspended-sediment sampling and laboratory analysis methods

    USGS Publications Warehouse

    Groten, Joel T.; Johnson, Gregory D.

    2018-03-06

    Accurate measurements of suspended sediment, a leading water-quality impairment in many Minnesota rivers, are important for managing and protecting water resources; however, water-quality standards for suspended sediment in Minnesota are based on grab field sampling and total suspended solids (TSS) laboratory analysis methods that have underrepresented concentrations of suspended sediment in rivers compared to U.S. Geological Survey equal-width-increment or equal-discharge-increment (EWDI) field sampling and suspended sediment concentration (SSC) laboratory analysis methods. Because of this underrepresentation, the U.S. Geological Survey, in collaboration with the Minnesota Pollution Control Agency, collected concurrent grab and EWDI samples at eight sites to compare results obtained using different combinations of field sampling and laboratory analysis methods.Study results determined that grab field sampling and TSS laboratory analysis results were biased substantially low compared to EWDI sampling and SSC laboratory analysis results, respectively. Differences in both field sampling and laboratory analysis methods caused grab and TSS methods to be biased substantially low. The difference in laboratory analysis methods was slightly greater than field sampling methods.Sand-sized particles had a strong effect on the comparability of the field sampling and laboratory analysis methods. These results indicated that grab field sampling and TSS laboratory analysis methods fail to capture most of the sand being transported by the stream. The results indicate there is less of a difference among samples collected with grab field sampling and analyzed for TSS and concentration of fines in SSC. Even though differences are present, the presence of strong correlations between SSC and TSS concentrations provides the opportunity to develop site specific relations to address transport processes not captured by grab field sampling and TSS laboratory analysis methods.

  13. Methods for sample size determination in cluster randomized trials

    PubMed Central

    Rutterford, Clare; Copas, Andrew; Eldridge, Sandra

    2015-01-01

    Background: The use of cluster randomized trials (CRTs) is increasing, along with the variety in their design and analysis. The simplest approach for their sample size calculation is to calculate the sample size assuming individual randomization and inflate this by a design effect to account for randomization by cluster. The assumptions of a simple design effect may not always be met; alternative or more complicated approaches are required. Methods: We summarise a wide range of sample size methods available for cluster randomized trials. For those familiar with sample size calculations for individually randomized trials but with less experience in the clustered case, this manuscript provides formulae for a wide range of scenarios with associated explanation and recommendations. For those with more experience, comprehensive summaries are provided that allow quick identification of methods for a given design, outcome and analysis method. Results: We present first those methods applicable to the simplest two-arm, parallel group, completely randomized design followed by methods that incorporate deviations from this design such as: variability in cluster sizes; attrition; non-compliance; or the inclusion of baseline covariates or repeated measures. The paper concludes with methods for alternative designs. Conclusions: There is a large amount of methodology available for sample size calculations in CRTs. This paper gives the most comprehensive description of published methodology for sample size calculation and provides an important resource for those designing these trials. PMID:26174515

  14. Out-of-Sample Extensions for Non-Parametric Kernel Methods.

    PubMed

    Pan, Binbin; Chen, Wen-Sheng; Chen, Bo; Xu, Chen; Lai, Jianhuang

    2017-02-01

    Choosing suitable kernels plays an important role in the performance of kernel methods. Recently, a number of studies were devoted to developing nonparametric kernels. Without assuming any parametric form of the target kernel, nonparametric kernel learning offers a flexible scheme to utilize the information of the data, which may potentially characterize the data similarity better. The kernel methods using nonparametric kernels are referred to as nonparametric kernel methods. However, many nonparametric kernel methods are restricted to transductive learning, where the prediction function is defined only over the data points given beforehand. They have no straightforward extension for the out-of-sample data points, and thus cannot be applied to inductive learning. In this paper, we show how to make the nonparametric kernel methods applicable to inductive learning. The key problem of out-of-sample extension is how to extend the nonparametric kernel matrix to the corresponding kernel function. A regression approach in the hyper reproducing kernel Hilbert space is proposed to solve this problem. Empirical results indicate that the out-of-sample performance is comparable to the in-sample performance in most cases. Experiments on face recognition demonstrate the superiority of our nonparametric kernel method over the state-of-the-art parametric kernel methods.

  15. Extended Importance Sampling for Reliability Analysis under Evidence Theory

    NASA Astrophysics Data System (ADS)

    Yuan, X. K.; Chen, B.; Zhang, B. Q.

    2018-05-01

    In early engineering practice, the lack of data and information makes uncertainty difficult to deal with. However, evidence theory has been proposed to handle uncertainty with limited information as an alternative way to traditional probability theory. In this contribution, a simulation-based approach, called ‘Extended importance sampling’, is proposed based on evidence theory to handle problems with epistemic uncertainty. The proposed approach stems from the traditional importance sampling for reliability analysis under probability theory, and is developed to handle the problem with epistemic uncertainty. It first introduces a nominal instrumental probability density function (PDF) for every epistemic uncertainty variable, and thus an ‘equivalent’ reliability problem under probability theory is obtained. Then the samples of these variables are generated in a way of importance sampling. Based on these samples, the plausibility and belief (upper and lower bounds of probability) can be estimated. It is more efficient than direct Monte Carlo simulation. Numerical and engineering examples are given to illustrate the efficiency and feasible of the proposed approach.

  16. Importance-sampling computation of statistical properties of coupled oscillators

    NASA Astrophysics Data System (ADS)

    Gupta, Shamik; Leitão, Jorge C.; Altmann, Eduardo G.

    2017-07-01

    We introduce and implement an importance-sampling Monte Carlo algorithm to study systems of globally coupled oscillators. Our computational method efficiently obtains estimates of the tails of the distribution of various measures of dynamical trajectories corresponding to states occurring with (exponentially) small probabilities. We demonstrate the general validity of our results by applying the method to two contrasting cases: the driven-dissipative Kuramoto model, a paradigm in the study of spontaneous synchronization; and the conservative Hamiltonian mean-field model, a prototypical system of long-range interactions. We present results for the distribution of the finite-time Lyapunov exponent and a time-averaged order parameter. Among other features, our results show most notably that the distributions exhibit a vanishing standard deviation but a skewness that is increasing in magnitude with the number of oscillators, implying that nontrivial asymmetries and states yielding rare or atypical values of the observables persist even for a large number of oscillators.

  17. 40 CFR 80.330 - What are the sampling and testing requirements for refiners and importers?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... an exemption under this section, upon notification from EPA, the refiner's exemption will be void ab initio. (b) Sampling methods. For purposes of paragraph (a) of this section, refiners and importers shall...

  18. 40 CFR 80.330 - What are the sampling and testing requirements for refiners and importers?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... an exemption under this section, upon notification from EPA, the refiner's exemption will be void ab initio. (b) Sampling methods. For purposes of paragraph (a) of this section, refiners and importers shall...

  19. 40 CFR 80.330 - What are the sampling and testing requirements for refiners and importers?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... an exemption under this section, upon notification from EPA, the refiner's exemption will be void ab initio. (b) Sampling methods. For purposes of paragraph (a) of this section, refiners and importers shall...

  20. 40 CFR 80.330 - What are the sampling and testing requirements for refiners and importers?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... an exemption under this section, upon notification from EPA, the refiner's exemption will be void ab initio. (b) Sampling methods. For purposes of paragraph (a) of this section, refiners and importers shall...

  1. 40 CFR 80.330 - What are the sampling and testing requirements for refiners and importers?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... an exemption under this section, upon notification from EPA, the refiner's exemption will be void ab initio. (b) Sampling methods. For purposes of paragraph (a) of this section, refiners and importers shall...

  2. Integrated Hamiltonian sampling: a simple and versatile method for free energy simulations and conformational sampling.

    PubMed

    Mori, Toshifumi; Hamers, Robert J; Pedersen, Joel A; Cui, Qiang

    2014-07-17

    Motivated by specific applications and the recent work of Gao and co-workers on integrated tempering sampling (ITS), we have developed a novel sampling approach referred to as integrated Hamiltonian sampling (IHS). IHS is straightforward to implement and complementary to existing methods for free energy simulation and enhanced configurational sampling. The method carries out sampling using an effective Hamiltonian constructed by integrating the Boltzmann distributions of a series of Hamiltonians. By judiciously selecting the weights of the different Hamiltonians, one achieves rapid transitions among the energy landscapes that underlie different Hamiltonians and therefore an efficient sampling of important regions of the conformational space. Along this line, IHS shares similar motivations as the enveloping distribution sampling (EDS) approach of van Gunsteren and co-workers, although the ways that distributions of different Hamiltonians are integrated are rather different in IHS and EDS. Specifically, we report efficient ways for determining the weights using a combination of histogram flattening and weighted histogram analysis approaches, which make it straightforward to include many end-state and intermediate Hamiltonians in IHS so as to enhance its flexibility. Using several relatively simple condensed phase examples, we illustrate the implementation and application of IHS as well as potential developments for the near future. The relation of IHS to several related sampling methods such as Hamiltonian replica exchange molecular dynamics and λ-dynamics is also briefly discussed.

  3. Moderate deviations-based importance sampling for stochastic recursive equations

    DOE PAGES

    Dupuis, Paul; Johnson, Dane

    2017-11-17

    Abstract Subsolutions to the Hamilton–Jacobi–Bellman equation associated with a moderate deviations approximation are used to design importance sampling changes of measure for stochastic recursive equations. Analogous to what has been done for large deviations subsolution-based importance sampling, these schemes are shown to be asymptotically optimal under the moderate deviations scaling. We present various implementations and numerical results to contrast their performance, and also discuss the circumstances under which a moderate deviation scaling might be appropriate.

  4. Moderate deviations-based importance sampling for stochastic recursive equations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dupuis, Paul; Johnson, Dane

    Abstract Subsolutions to the Hamilton–Jacobi–Bellman equation associated with a moderate deviations approximation are used to design importance sampling changes of measure for stochastic recursive equations. Analogous to what has been done for large deviations subsolution-based importance sampling, these schemes are shown to be asymptotically optimal under the moderate deviations scaling. We present various implementations and numerical results to contrast their performance, and also discuss the circumstances under which a moderate deviation scaling might be appropriate.

  5. A quantitative evaluation of two methods for preserving hair samples

    USGS Publications Warehouse

    Roon, David A.; Waits, L.P.; Kendall, K.C.

    2003-01-01

    Hair samples are an increasingly important DNA source for wildlife studies, yet optimal storage methods and DNA degradation rates have not been rigorously evaluated. We tested amplification success rates over a one-year storage period for DNA extracted from brown bear (Ursus arctos) hair samples preserved using silica desiccation and -20C freezing. For three nuclear DNA microsatellites, success rates decreased significantly after a six-month time point, regardless of storage method. For a 1000 bp mitochondrial fragment, a similar decrease occurred after a two-week time point. Minimizing delays between collection and DNA extraction will maximize success rates for hair-based noninvasive genetic sampling projects.

  6. Coalescent: an open-science framework for importance sampling in coalescent theory.

    PubMed

    Tewari, Susanta; Spouge, John L

    2015-01-01

    Background. In coalescent theory, computer programs often use importance sampling to calculate likelihoods and other statistical quantities. An importance sampling scheme can exploit human intuition to improve statistical efficiency of computations, but unfortunately, in the absence of general computer frameworks on importance sampling, researchers often struggle to translate new sampling schemes computationally or benchmark against different schemes, in a manner that is reliable and maintainable. Moreover, most studies use computer programs lacking a convenient user interface or the flexibility to meet the current demands of open science. In particular, current computer frameworks can only evaluate the efficiency of a single importance sampling scheme or compare the efficiencies of different schemes in an ad hoc manner. Results. We have designed a general framework (http://coalescent.sourceforge.net; language: Java; License: GPLv3) for importance sampling that computes likelihoods under the standard neutral coalescent model of a single, well-mixed population of constant size over time following infinite sites model of mutation. The framework models the necessary core concepts, comes integrated with several data sets of varying size, implements the standard competing proposals, and integrates tightly with our previous framework for calculating exact probabilities. For a given dataset, it computes the likelihood and provides the maximum likelihood estimate of the mutation parameter. Well-known benchmarks in the coalescent literature validate the accuracy of the framework. The framework provides an intuitive user interface with minimal clutter. For performance, the framework switches automatically to modern multicore hardware, if available. It runs on three major platforms (Windows, Mac and Linux). Extensive tests and coverage make the framework reliable and maintainable. Conclusions. In coalescent theory, many studies of computational efficiency consider only

  7. 21 CFR 601.15 - Foreign establishments and products: samples for each importation.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Foreign establishments and products: samples for each importation. 601.15 Section 601.15 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... establishments and products: samples for each importation. Random samples of each importation, obtained by the...

  8. 21 CFR 601.15 - Foreign establishments and products: samples for each importation.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 7 2011-04-01 2010-04-01 true Foreign establishments and products: samples for each importation. 601.15 Section 601.15 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... establishments and products: samples for each importation. Random samples of each importation, obtained by the...

  9. Improved Sampling Method Reduces Isokinetic Sampling Errors.

    ERIC Educational Resources Information Center

    Karels, Gale G.

    The particulate sampling system currently in use by the Bay Area Air Pollution Control District, San Francisco, California is described in this presentation for the 12th Conference on Methods in Air Pollution and Industrial Hygiene Studies, University of Southern California, April, 1971. The method represents a practical, inexpensive tool that can…

  10. On the importance of incorporating sampling weights in ...

    EPA Pesticide Factsheets

    Occupancy models are used extensively to assess wildlife-habitat associations and to predict species distributions across large geographic regions. Occupancy models were developed as a tool to properly account for imperfect detection of a species. Current guidelines on survey design requirements for occupancy models focus on the number of sample units and the pattern of revisits to a sample unit within a season. We focus on the sampling design or how the sample units are selected in geographic space (e.g., stratified, simple random, unequal probability, etc). In a probability design, each sample unit has a sample weight which quantifies the number of sample units it represents in the finite (oftentimes areal) sampling frame. We demonstrate the importance of including sampling weights in occupancy model estimation when the design is not a simple random sample or equal probability design. We assume a finite areal sampling frame as proposed for a national bat monitoring program. We compare several unequal and equal probability designs and varying sampling intensity within a simulation study. We found the traditional single season occupancy model produced biased estimates of occupancy and lower confidence interval coverage rates compared to occupancy models that accounted for the sampling design. We also discuss how our findings inform the analyses proposed for the nascent North American Bat Monitoring Program and other collaborative synthesis efforts that propose h

  11. Efficiency of snake sampling methods in the Brazilian semiarid region.

    PubMed

    Mesquita, Paula C M D; Passos, Daniel C; Cechin, Sonia Z

    2013-09-01

    The choice of sampling methods is a crucial step in every field survey in herpetology. In countries where time and financial support are limited, the choice of the methods is critical. The methods used to sample snakes often lack objective criteria, and the traditional methods have apparently been more important when making the choice. Consequently researches using not-standardized methods are frequently found in the literature. We have compared four commonly used methods for sampling snake assemblages in a semiarid area in Brazil. We compared the efficacy of each method based on the cost-benefit regarding the number of individuals and species captured, time, and financial investment. We found that pitfall traps were the less effective method in all aspects that were evaluated and it was not complementary to the other methods in terms of abundance of species and assemblage structure. We conclude that methods can only be considered complementary if they are standardized to the objectives of the study. The use of pitfall traps in short-term surveys of the snake fauna in areas with shrubby vegetation and stony soil is not recommended.

  12. Comparing two sampling methods to engage hard-to-reach communities in research priority setting.

    PubMed

    Valerio, Melissa A; Rodriguez, Natalia; Winkler, Paula; Lopez, Jaime; Dennison, Meagen; Liang, Yuanyuan; Turner, Barbara J

    2016-10-28

    Effective community-partnered and patient-centered outcomes research needs to address community priorities. However, optimal sampling methods to engage stakeholders from hard-to-reach, vulnerable communities to generate research priorities have not been identified. In two similar rural, largely Hispanic communities, a community advisory board guided recruitment of stakeholders affected by chronic pain using a different method in each community: 1) snowball sampling, a chain- referral method or 2) purposive sampling to recruit diverse stakeholders. In both communities, three groups of stakeholders attended a series of three facilitated meetings to orient, brainstorm, and prioritize ideas (9 meetings/community). Using mixed methods analysis, we compared stakeholder recruitment and retention as well as priorities from both communities' stakeholders on mean ratings of their ideas based on importance and feasibility for implementation in their community. Of 65 eligible stakeholders in one community recruited by snowball sampling, 55 (85 %) consented, 52 (95 %) attended the first meeting, and 36 (65 %) attended all 3 meetings. In the second community, the purposive sampling method was supplemented by convenience sampling to increase recruitment. Of 69 stakeholders recruited by this combined strategy, 62 (90 %) consented, 36 (58 %) attended the first meeting, and 26 (42 %) attended all 3 meetings. Snowball sampling recruited more Hispanics and disabled persons (all P < 0.05). Despite differing recruitment strategies, stakeholders from the two communities identified largely similar ideas for research, focusing on non-pharmacologic interventions for management of chronic pain. Ratings on importance and feasibility for community implementation differed only on the importance of massage services (P = 0.045) which was higher for the purposive/convenience sampling group and for city improvements/transportation services (P = 0.004) which was higher for the

  13. Volatile organic compounds: sampling methods and their worldwide profile in ambient air.

    PubMed

    Kumar, Anuj; Víden, Ivan

    2007-08-01

    The atmosphere is a particularly difficult analytical system because of the very low levels of substances to be analysed, sharp variations in pollutant levels with time and location, differences in wind, temperature and humidity. This makes the selection of an efficient sampling technique for air analysis a key step to reliable results. Generally, methods for volatile organic compounds sampling include collection of the whole air or preconcentration of samples on adsorbents. All the methods vary from each other according to the sampling technique, type of sorbent, method of extraction and identification technique. In this review paper we discuss various important aspects for sampling of volatile organic compounds by the widely used and advanced sampling methods. Characteristics of various adsorbents used for VOCs sampling are also described. Furthermore, this paper makes an effort to comprehensively review the concentration levels of volatile organic compounds along with the methodology used for analysis, in major cities of the world.

  14. Characterizing lentic freshwater fish assemblages using multiple sampling methods

    USGS Publications Warehouse

    Fischer, Jesse R.; Quist, Michael C.

    2014-01-01

    Characterizing fish assemblages in lentic ecosystems is difficult, and multiple sampling methods are almost always necessary to gain reliable estimates of indices such as species richness. However, most research focused on lentic fish sampling methodology has targeted recreationally important species, and little to no information is available regarding the influence of multiple methods and timing (i.e., temporal variation) on characterizing entire fish assemblages. Therefore, six lakes and impoundments (48–1,557 ha surface area) were sampled seasonally with seven gear types to evaluate the combined influence of sampling methods and timing on the number of species and individuals sampled. Probabilities of detection for species indicated strong selectivities and seasonal trends that provide guidance on optimal seasons to use gears when targeting multiple species. The evaluation of species richness and number of individuals sampled using multiple gear combinations demonstrated that appreciable benefits over relatively few gears (e.g., to four) used in optimal seasons were not present. Specifically, over 90 % of the species encountered with all gear types and season combinations (N = 19) from six lakes and reservoirs were sampled with nighttime boat electrofishing in the fall and benthic trawling, modified-fyke, and mini-fyke netting during the summer. Our results indicated that the characterization of lentic fish assemblages was highly influenced by the selection of sampling gears and seasons, but did not appear to be influenced by waterbody type (i.e., natural lake, impoundment). The standardization of data collected with multiple methods and seasons to account for bias is imperative to monitoring of lentic ecosystems and will provide researchers with increased reliability in their interpretations and decisions made using information on lentic fish assemblages.

  15. Sampling system and method

    DOEpatents

    Decker, David L.; Lyles, Brad F.; Purcell, Richard G.; Hershey, Ronald Lee

    2013-04-16

    The present disclosure provides an apparatus and method for coupling conduit segments together. A first pump obtains a sample and transmits it through a first conduit to a reservoir accessible by a second pump. The second pump further conducts the sample from the reservoir through a second conduit.

  16. Importance sampling with imperfect cloning for the computation of generalized Lyapunov exponents

    NASA Astrophysics Data System (ADS)

    Anteneodo, Celia; Camargo, Sabrina; Vallejos, Raúl O.

    2017-12-01

    We revisit the numerical calculation of generalized Lyapunov exponents, L (q ) , in deterministic dynamical systems. The standard method consists of adding noise to the dynamics in order to use importance sampling algorithms. Then L (q ) is obtained by taking the limit noise-amplitude → 0 after the calculation. We focus on a particular method that involves periodic cloning and pruning of a set of trajectories. However, instead of considering a noisy dynamics, we implement an imperfect (noisy) cloning. This alternative method is compared with the standard one and, when possible, with analytical results. As a workbench we use the asymmetric tent map, the standard map, and a system of coupled symplectic maps. The general conclusion of this study is that the imperfect-cloning method performs as well as the standard one, with the advantage of preserving the deterministic dynamics.

  17. Evaluation of seven aquatic sampling methods for amphibians and other aquatic fauna

    USGS Publications Warehouse

    Gunzburger, M.S.

    2007-01-01

    To design effective and efficient research and monitoring programs researchers must have a thorough understanding of the capabilities and limitations of their sampling methods. Few direct comparative studies exist for aquatic sampling methods for amphibians. The objective of this study was to simultaneously employ seven aquatic sampling methods in 10 wetlands to compare amphibian species richness and number of individuals detected with each method. Four sampling methods allowed counts of individuals (metal dipnet, D-frame dipnet, box trap, crayfish trap), whereas the other three methods allowed detection of species (visual encounter, aural, and froglogger). Amphibian species richness was greatest with froglogger, box trap, and aural samples. For anuran species, the sampling methods by which each life stage was detected was related to relative length of larval and breeding periods and tadpole size. Detection probability of amphibians varied across sampling methods. Box trap sampling resulted in the most precise amphibian count, but the precision of all four count-based methods was low (coefficient of variation > 145 for all methods). The efficacy of the four count sampling methods at sampling fish and aquatic invertebrates was also analyzed because these predatory taxa are known to be important predictors of amphibian habitat distribution. Species richness and counts were similar for fish with the four methods, whereas invertebrate species richness and counts were greatest in box traps. An effective wetland amphibian monitoring program in the southeastern United States should include multiple sampling methods to obtain the most accurate assessment of species community composition at each site. The combined use of frogloggers, crayfish traps, and dipnets may be the most efficient and effective amphibian monitoring protocol. ?? 2007 Brill Academic Publishers.

  18. Time-dependent importance sampling in semiclassical initial value representation calculations for time correlation functions. II. A simplified implementation.

    PubMed

    Tao, Guohua; Miller, William H

    2012-09-28

    An efficient time-dependent (TD) Monte Carlo (MC) importance sampling method has recently been developed [G. Tao and W. H. Miller, J. Chem. Phys. 135, 024104 (2011)] for the evaluation of time correlation functions using the semiclassical (SC) initial value representation (IVR) methodology. In this TD-SC-IVR method, the MC sampling uses information from both time-evolved phase points as well as their initial values, and only the "important" trajectories are sampled frequently. Even though the TD-SC-IVR was shown in some benchmark examples to be much more efficient than the traditional time-independent sampling method (which uses only initial conditions), the calculation of the SC prefactor-which is computationally expensive, especially for large systems-is still required for accepted trajectories. In the present work, we present an approximate implementation of the TD-SC-IVR method that is completely prefactor-free; it gives the time correlation function as a classical-like magnitude function multiplied by a phase function. Application of this approach to flux-flux correlation functions (which yield reaction rate constants) for the benchmark H + H(2) system shows very good agreement with exact quantum results. Limitations of the approximate approach are also discussed.

  19. Universal nucleic acids sample preparation method for cells, spores and their mixture

    DOEpatents

    Bavykin, Sergei [Darien, IL

    2011-01-18

    The present invention relates to a method for extracting nucleic acids from biological samples. More specifically the invention relates to a universal method for extracting nucleic acids from unidentified biological samples. An advantage of the presently invented method is its ability to effectively and efficiently extract nucleic acids from a variety of different cell types including but not limited to prokaryotic or eukaryotic cells and/or recalcitrant organisms (i.e. spores). Unlike prior art methods which are focused on extracting nucleic acids from vegetative cell or spores, the present invention effectively extracts nucleic acids from spores, multiple cell types or mixtures thereof using a single method. Important that the invented method has demonstrated an ability to extract nucleic acids from spores and vegetative bacterial cells with similar levels effectiveness. The invented method employs a multi-step protocol which erodes the cell structure of the biological sample, isolates, labels, fragments nucleic acids and purifies labeled samples from the excess of dye.

  20. Subrandom methods for multidimensional nonuniform sampling.

    PubMed

    Worley, Bradley

    2016-08-01

    Methods of nonuniform sampling that utilize pseudorandom number sequences to select points from a weighted Nyquist grid are commonplace in biomolecular NMR studies, due to the beneficial incoherence introduced by pseudorandom sampling. However, these methods require the specification of a non-arbitrary seed number in order to initialize a pseudorandom number generator. Because the performance of pseudorandom sampling schedules can substantially vary based on seed number, this can complicate the task of routine data collection. Approaches such as jittered sampling and stochastic gap sampling are effective at reducing random seed dependence of nonuniform sampling schedules, but still require the specification of a seed number. This work formalizes the use of subrandom number sequences in nonuniform sampling as a means of seed-independent sampling, and compares the performance of three subrandom methods to their pseudorandom counterparts using commonly applied schedule performance metrics. Reconstruction results using experimental datasets are also provided to validate claims made using these performance metrics. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Method and apparatus for data sampling

    DOEpatents

    Odell, Daniel M. C.

    1994-01-01

    A method and apparatus for sampling radiation detector outputs and determining event data from the collected samples. The method uses high speed sampling of the detector output, the conversion of the samples to digital values, and the discrimination of the digital values so that digital values representing detected events are determined. The high speed sampling and digital conversion is performed by an A/D sampler that samples the detector output at a rate high enough to produce numerous digital samples for each detected event. The digital discrimination identifies those digital samples that are not representative of detected events. The sampling and discrimination also provides for temporary or permanent storage, either serially or in parallel, to a digital storage medium.

  2. The experience sampling method: Investigating students' affective experience

    NASA Astrophysics Data System (ADS)

    Nissen, Jayson M.; Stetzer, MacKenzie R.; Shemwell, Jonathan T.

    2013-01-01

    Improving non-cognitive outcomes such as attitudes, efficacy, and persistence in physics courses is an important goal of physics education. This investigation implemented an in-the-moment surveying technique called the Experience Sampling Method (ESM) [1] to measure students' affective experience in physics. Measurements included: self-efficacy, cognitive efficiency, activation, intrinsic motivation, and affect. Data are presented that show contrasts in students' experiences (e.g., in physics vs. non-physics courses).

  3. Method and apparatus for data sampling

    DOEpatents

    Odell, D.M.C.

    1994-04-19

    A method and apparatus for sampling radiation detector outputs and determining event data from the collected samples is described. The method uses high speed sampling of the detector output, the conversion of the samples to digital values, and the discrimination of the digital values so that digital values representing detected events are determined. The high speed sampling and digital conversion is performed by an A/D sampler that samples the detector output at a rate high enough to produce numerous digital samples for each detected event. The digital discrimination identifies those digital samples that are not representative of detected events. The sampling and discrimination also provides for temporary or permanent storage, either serially or in parallel, to a digital storage medium. 6 figures.

  4. Importance Sampling of Word Patterns in DNA and Protein Sequences

    PubMed Central

    Chan, Hock Peng; Chen, Louis H.Y.

    2010-01-01

    Abstract Monte Carlo methods can provide accurate p-value estimates of word counting test statistics and are easy to implement. They are especially attractive when an asymptotic theory is absent or when either the search sequence or the word pattern is too short for the application of asymptotic formulae. Naive direct Monte Carlo is undesirable for the estimation of small probabilities because the associated rare events of interest are seldom generated. We propose instead efficient importance sampling algorithms that use controlled insertion of the desired word patterns on randomly generated sequences. The implementation is illustrated on word patterns of biological interest: palindromes and inverted repeats, patterns arising from position-specific weight matrices (PSWMs), and co-occurrences of pairs of motifs. PMID:21128856

  5. Rapid method for the determination of 226Ra in hydraulic fracturing wastewater samples

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Maxwell, Sherrod L.; Culligan, Brian K.; Warren, Richard A.

    A new method that rapidly preconcentrates and measures 226Ra from hydraulic fracturing wastewater samples was developed in the Savannah River Environmental Laboratory. The method improves the quality of 226Ra measurements using gamma spectrometry by providing up to 100x preconcentration of 226Ra from this difficult sample matrix, which contains very high levels of calcium, barium, strontium, magnesium and sodium. The high chemical yield, typically 80-90%, facilitates a low detection limit, important for lower level samples, and indicates method ruggedness. Ba-133 tracer is used to determine chemical yield and correct for geometry-related counting issues. The 226Ra sample preparation takes < 2 hours.

  6. Rapid method for the determination of 226Ra in hydraulic fracturing wastewater samples

    DOE PAGES

    Maxwell, Sherrod L.; Culligan, Brian K.; Warren, Richard A.; ...

    2016-03-24

    A new method that rapidly preconcentrates and measures 226Ra from hydraulic fracturing wastewater samples was developed in the Savannah River Environmental Laboratory. The method improves the quality of 226Ra measurements using gamma spectrometry by providing up to 100x preconcentration of 226Ra from this difficult sample matrix, which contains very high levels of calcium, barium, strontium, magnesium and sodium. The high chemical yield, typically 80-90%, facilitates a low detection limit, important for lower level samples, and indicates method ruggedness. Ba-133 tracer is used to determine chemical yield and correct for geometry-related counting issues. The 226Ra sample preparation takes < 2 hours.

  7. Sampling system and method

    DOEpatents

    Decker, David L.; Lyles, Brad F.; Purcell, Richard G.; Hershey, Ronald Lee

    2017-03-07

    In one embodiment, the present disclosure provides an apparatus and method for supporting a tubing bundle during installation or removal. The apparatus includes a clamp for securing the tubing bundle to an external wireline. In various examples, the clamp is external to the tubing bundle or integral with the tubing bundle. According to one method, a tubing bundle and wireline are deployed together and the tubing bundle periodically secured to the wireline using a clamp. In another embodiment, the present disclosure provides an apparatus and method for coupling conduit segments together. A first pump obtains a sample and transmits it through a first conduit to a reservoir accessible by a second pump. The second pump further conducts the sample from the reservoir through a second conduit. In a specific example, one or more clamps are used to connect the first and/or second conduits to an external wireline.

  8. Classifying Imbalanced Data Streams via Dynamic Feature Group Weighting with Importance Sampling.

    PubMed

    Wu, Ke; Edwards, Andrea; Fan, Wei; Gao, Jing; Zhang, Kun

    2014-04-01

    Data stream classification and imbalanced data learning are two important areas of data mining research. Each has been well studied to date with many interesting algorithms developed. However, only a few approaches reported in literature address the intersection of these two fields due to their complex interplay. In this work, we proposed an importance sampling driven, dynamic feature group weighting framework (DFGW-IS) for classifying data streams of imbalanced distribution. Two components are tightly incorporated into the proposed approach to address the intrinsic characteristics of concept-drifting, imbalanced streaming data. Specifically, the ever-evolving concepts are tackled by a weighted ensemble trained on a set of feature groups with each sub-classifier (i.e. a single classifier or an ensemble) weighed by its discriminative power and stable level. The un-even class distribution, on the other hand, is typically battled by the sub-classifier built in a specific feature group with the underlying distribution rebalanced by the importance sampling technique. We derived the theoretical upper bound for the generalization error of the proposed algorithm. We also studied the empirical performance of our method on a set of benchmark synthetic and real world data, and significant improvement has been achieved over the competing algorithms in terms of standard evaluation metrics and parallel running time. Algorithm implementations and datasets are available upon request.

  9. A new sampling method for fibre length measurement

    NASA Astrophysics Data System (ADS)

    Wu, Hongyan; Li, Xianghong; Zhang, Junying

    2018-06-01

    This paper presents a new sampling method for fibre length measurement. This new method can meet the three features of an effective sampling method, also it can produce the beard with two symmetrical ends which can be scanned from the holding line to get two full fibrograms for each sample. The methodology was introduced and experiments were performed to investigate effectiveness of the new method. The results show that the new sampling method is an effective sampling method.

  10. The study of combining Latin Hypercube Sampling method and LU decomposition method (LULHS method) for constructing spatial random field

    NASA Astrophysics Data System (ADS)

    WANG, P. T.

    2015-12-01

    Groundwater modeling requires to assign hydrogeological properties to every numerical grid. Due to the lack of detailed information and the inherent spatial heterogeneity, geological properties can be treated as random variables. Hydrogeological property is assumed to be a multivariate distribution with spatial correlations. By sampling random numbers from a given statistical distribution and assigning a value to each grid, a random field for modeling can be completed. Therefore, statistics sampling plays an important role in the efficiency of modeling procedure. Latin Hypercube Sampling (LHS) is a stratified random sampling procedure that provides an efficient way to sample variables from their multivariate distributions. This study combines the the stratified random procedure from LHS and the simulation by using LU decomposition to form LULHS. Both conditional and unconditional simulations of LULHS were develpoed. The simulation efficiency and spatial correlation of LULHS are compared to the other three different simulation methods. The results show that for the conditional simulation and unconditional simulation, LULHS method is more efficient in terms of computational effort. Less realizations are required to achieve the required statistical accuracy and spatial correlation.

  11. Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

    PubMed Central

    White, James Robert; Nagarajan, Niranjan; Pop, Mihai

    2009-01-01

    Numerous studies are currently underway to characterize the microbial communities inhabiting our world. These studies aim to dramatically expand our understanding of the microbial biosphere and, more importantly, hope to reveal the secrets of the complex symbiotic relationship between us and our commensal bacterial microflora. An important prerequisite for such discoveries are computational tools that are able to rapidly and accurately compare large datasets generated from complex bacterial communities to identify features that distinguish them. We present a statistical method for comparing clinical metagenomic samples from two treatment populations on the basis of count data (e.g. as obtained through sequencing) to detect differentially abundant features. Our method, Metastats, employs the false discovery rate to improve specificity in high-complexity environments, and separately handles sparsely-sampled features using Fisher's exact test. Under a variety of simulations, we show that Metastats performs well compared to previously used methods, and significantly outperforms other methods for features with sparse counts. We demonstrate the utility of our method on several datasets including a 16S rRNA survey of obese and lean human gut microbiomes, COG functional profiles of infant and mature gut microbiomes, and bacterial and viral metabolic subsystem data inferred from random sequencing of 85 metagenomes. The application of our method to the obesity dataset reveals differences between obese and lean subjects not reported in the original study. For the COG and subsystem datasets, we provide the first statistically rigorous assessment of the differences between these populations. The methods described in this paper are the first to address clinical metagenomic datasets comprising samples from multiple subjects. Our methods are robust across datasets of varied complexity and sampling level. While designed for metagenomic applications, our software can also be applied

  12. Profiling Cholinesterase Adduction: A High-Throughput Prioritization Method for Organophosphate Exposure Samples

    PubMed Central

    Carter, Melissa D.; Crow, Brian S.; Pantazides, Brooke G.; Watson, Caroline M.; deCastro, B. Rey; Thomas, Jerry D.; Blake, Thomas A.; Johnson, Rudolph C.

    2017-01-01

    A high-throughput prioritization method was developed for use with a validated confirmatory method detecting organophosphorus nerve agent exposure by immunomagnetic separation-HPLC-MS/MS. A ballistic gradient was incorporated into this analytical method in order to profile unadducted butyrylcholinesterase (BChE) in clinical samples. With Zhang, et al. 1999’s Z′-factor of 0.88 ± 0.01 (SD) of control analytes and Z-factor of 0.25 ± 0.06 (SD) of serum samples, the assay is rated an “excellent assay” for the synthetic peptide controls used and a “double assay” when used to prioritize clinical samples. Hits, defined as samples containing BChE Ser-198 adducts or no BChE present, were analyzed in a confirmatory method for identification and quantitation of the BChE adduct, if present. The ability to prioritize samples by highest exposure for confirmatory analysis is of particular importance in an exposure to cholinesterase inhibitors such as organophosphorus nerve agents where a large number of clinical samples may be collected. In an initial blind screen, 67 out of 70 samples were accurately identified giving an assay accuracy of 96% and yielded no false negatives. The method is the first to provide a high-throughput prioritization assay for profiling adduction of Ser-198 BChE in clinical samples. PMID:23954929

  13. Soil sampling kit and a method of sampling therewith

    DOEpatents

    Thompson, Cyril V.

    1991-01-01

    A soil sampling device and a sample containment device for containing a soil sample is disclosed. In addition, a method for taking a soil sample using the soil sampling device and soil sample containment device to minimize the loss of any volatile organic compounds contained in the soil sample prior to analysis is disclosed. The soil sampling device comprises two close fitting, longitudinal tubular members of suitable length, the inner tube having the outward end closed. With the inner closed tube withdrawn a selected distance, the outer tube can be inserted into the ground or other similar soft material to withdraw a sample of material for examination. The inner closed end tube controls the volume of the sample taken and also serves to eject the sample. The soil sample containment device has a sealing member which is adapted to attach to an analytical apparatus which analyzes the volatile organic compounds contained in the sample. The soil sampling device in combination with the soil sample containment device allow an operator to obtain a soil sample containing volatile organic compounds and minimizing the loss of the volatile organic compounds prior to analysis of the soil sample for the volatile organic compounds.

  14. Apparatus and method for handheld sampling

    DOEpatents

    Staab, Torsten A.

    2005-09-20

    The present invention includes an apparatus, and corresponding method, for taking a sample. The apparatus is built around a frame designed to be held in at least one hand. A sample media is used to secure the sample. A sample media adapter for securing the sample media is operated by a trigger mechanism connectively attached within the frame to the sample media adapter.

  15. Performance of sampling methods to estimate log characteristics for wildlife.

    Treesearch

    Lisa J. Bate; Torolf R. Torgersen; Michael J. Wisdom; Edward O. Garton

    2004-01-01

    Accurate estimation of the characteristics of log resources, or coarse woody debris (CWD), is critical to effective management of wildlife and other forest resources. Despite the importance of logs as wildlife habitat, methods for sampling logs have traditionally focused on silvicultural and fire applications. These applications have emphasized estimates of log volume...

  16. A LITERATURE REVIEW OF WIPE SAMPLING METHODS FOR CHEMICAL WARFARE AGENTS AND TOXIC INDUSTRIAL CHEMICALS

    EPA Science Inventory

    Wipe sampling is an important technique for the estimation of contaminant deposition in buildings, homes, or outdoor surfaces as a source of possible human exposure. Numerous

    methods of wipe sampling exist, and each method has its own specification for the type of wipe, we...

  17. Active Search on Carcasses versus Pitfall Traps: a Comparison of Sampling Methods.

    PubMed

    Zanetti, N I; Camina, R; Visciarelli, E C; Centeno, N D

    2016-04-01

    The study of insect succession in cadavers and the classification of arthropods have mostly been done by placing a carcass in a cage, protected from vertebrate scavengers, which is then visited periodically. An alternative is to use specific traps. Few studies on carrion ecology and forensic entomology involving the carcasses of large vertebrates have employed pitfall traps. The aims of this study were to compare both sampling methods (active search on a carcass and pitfall trapping) for each coleopteran family, and to establish whether there is a discrepancy (underestimation and/or overestimation) in the presence of each family by either method. A great discrepancy was found for almost all families with some of them being more abundant in samples obtained through active search on carcasses and others in samples from traps, whereas two families did not show any bias towards a given sampling method. The fact that families may be underestimated or overestimated by the type of sampling technique highlights the importance of combining both methods, active search on carcasses and pitfall traps, in order to obtain more complete information on decomposition, carrion habitat and cadaveric families or species. Furthermore, a hypothesis advanced on the reasons for the underestimation by either sampling method showing biases towards certain families. Information about the sampling techniques indicating which would be more appropriate to detect or find a particular family is provided.

  18. Soil sampling kit and a method of sampling therewith

    DOEpatents

    Thompson, C.V.

    1991-02-05

    A soil sampling device and a sample containment device for containing a soil sample is disclosed. In addition, a method for taking a soil sample using the soil sampling device and soil sample containment device to minimize the loss of any volatile organic compounds contained in the soil sample prior to analysis is disclosed. The soil sampling device comprises two close fitting, longitudinal tubular members of suitable length, the inner tube having the outward end closed. With the inner closed tube withdrawn a selected distance, the outer tube can be inserted into the ground or other similar soft material to withdraw a sample of material for examination. The inner closed end tube controls the volume of the sample taken and also serves to eject the sample. The soil sample containment device has a sealing member which is adapted to attach to an analytical apparatus which analyzes the volatile organic compounds contained in the sample. The soil sampling device in combination with the soil sample containment device allows an operator to obtain a soil sample containing volatile organic compounds and minimizing the loss of the volatile organic compounds prior to analysis of the soil sample for the volatile organic compounds. 11 figures.

  19. Different methods for volatile sampling in mammals

    PubMed Central

    Möller, Manfred; Marcillo, Andrea; Einspanier, Almuth; Weiß, Brigitte M.

    2017-01-01

    Previous studies showed that olfactory cues are important for mammalian communication. However, many specific compounds that convey information between conspecifics are still unknown. To understand mechanisms and functions of olfactory cues, olfactory signals such as volatile compounds emitted from individuals need to be assessed. Sampling of animals with and without scent glands was typically conducted using cotton swabs rubbed over the skin or fur and analysed by gas chromatography-mass spectrometry (GC-MS). However, this method has various drawbacks, including a high level of contaminations. Thus, we adapted two methods of volatile sampling from other research fields and compared them to sampling with cotton swabs. To do so we assessed the body odor of common marmosets (Callithrix jacchus) using cotton swabs, thermal desorption (TD) tubes and, alternatively, a mobile GC-MS device containing a thermal desorption trap. Overall, TD tubes comprised most compounds (N = 113), with half of those compounds being volatile (N = 52). The mobile GC-MS captured the fewest compounds (N = 35), of which all were volatile. Cotton swabs contained an intermediate number of compounds (N = 55), but very few volatiles (N = 10). Almost all compounds found with the mobile GC-MS were also captured with TD tubes (94%). Hence, we recommend TD tubes for state of the art sampling of body odor of mammals or other vertebrates, particularly for field studies, as they can be easily transported, stored and analysed with high performance instruments in the lab. Nevertheless, cotton swabs capture compounds which still may contribute to the body odor, e.g. after bacterial fermentation, while profiles from mobile GC-MS include only the most abundant volatiles of the body odor. PMID:28841690

  20. Detecting spatial structures in throughfall data: The effect of extent, sample size, sampling design, and variogram estimation method

    NASA Astrophysics Data System (ADS)

    Voss, Sebastian; Zimmermann, Beate; Zimmermann, Alexander

    2016-09-01

    In the last decades, an increasing number of studies analyzed spatial patterns in throughfall by means of variograms. The estimation of the variogram from sample data requires an appropriate sampling scheme: most importantly, a large sample and a layout of sampling locations that often has to serve both variogram estimation and geostatistical prediction. While some recommendations on these aspects exist, they focus on Gaussian data and high ratios of the variogram range to the extent of the study area. However, many hydrological data, and throughfall data in particular, do not follow a Gaussian distribution. In this study, we examined the effect of extent, sample size, sampling design, and calculation method on variogram estimation of throughfall data. For our investigation, we first generated non-Gaussian random fields based on throughfall data with large outliers. Subsequently, we sampled the fields with three extents (plots with edge lengths of 25 m, 50 m, and 100 m), four common sampling designs (two grid-based layouts, transect and random sampling) and five sample sizes (50, 100, 150, 200, 400). We then estimated the variogram parameters by method-of-moments (non-robust and robust estimators) and residual maximum likelihood. Our key findings are threefold. First, the choice of the extent has a substantial influence on the estimation of the variogram. A comparatively small ratio of the extent to the correlation length is beneficial for variogram estimation. Second, a combination of a minimum sample size of 150, a design that ensures the sampling of small distances and variogram estimation by residual maximum likelihood offers a good compromise between accuracy and efficiency. Third, studies relying on method-of-moments based variogram estimation may have to employ at least 200 sampling points for reliable variogram estimates. These suggested sample sizes exceed the number recommended by studies dealing with Gaussian data by up to 100 %. Given that most previous

  1. 7 CFR 29.110 - Method of sampling.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Method of sampling. 29.110 Section 29.110 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... INSPECTION Regulations Inspectors, Samplers, and Weighers § 29.110 Method of sampling. In sampling tobacco...

  2. 7 CFR 29.110 - Method of sampling.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Method of sampling. 29.110 Section 29.110 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... INSPECTION Regulations Inspectors, Samplers, and Weighers § 29.110 Method of sampling. In sampling tobacco...

  3. Uniform Sampling Table Method and its Applications II--Evaluating the Uniform Sampling by Experiment.

    PubMed

    Chen, Yibin; Chen, Jiaxi; Chen, Xuan; Wang, Min; Wang, Wei

    2015-01-01

    A new method of uniform sampling is evaluated in this paper. The items and indexes were adopted to evaluate the rationality of the uniform sampling. The evaluation items included convenience of operation, uniformity of sampling site distribution, and accuracy and precision of measured results. The evaluation indexes included operational complexity, occupation rate of sampling site in a row and column, relative accuracy of pill weight, and relative deviation of pill weight. They were obtained from three kinds of drugs with different shape and size by four kinds of sampling methods. Gray correlation analysis was adopted to make the comprehensive evaluation by comparing it with the standard method. The experimental results showed that the convenience of uniform sampling method was 1 (100%), odds ratio of occupation rate in a row and column was infinity, relative accuracy was 99.50-99.89%, reproducibility RSD was 0.45-0.89%, and weighted incidence degree exceeded the standard method. Hence, the uniform sampling method was easy to operate, and the selected samples were distributed uniformly. The experimental results demonstrated that the uniform sampling method has good accuracy and reproducibility, which can be put into use in drugs analysis.

  4. Importance sampling large deviations in nonequilibrium steady states. I.

    PubMed

    Ray, Ushnish; Chan, Garnet Kin-Lic; Limmer, David T

    2018-03-28

    Large deviation functions contain information on the stability and response of systems driven into nonequilibrium steady states and in such a way are similar to free energies for systems at equilibrium. As with equilibrium free energies, evaluating large deviation functions numerically for all but the simplest systems is difficult because by construction they depend on exponentially rare events. In this first paper of a series, we evaluate different trajectory-based sampling methods capable of computing large deviation functions of time integrated observables within nonequilibrium steady states. We illustrate some convergence criteria and best practices using a number of different models, including a biased Brownian walker, a driven lattice gas, and a model of self-assembly. We show how two popular methods for sampling trajectory ensembles, transition path sampling and diffusion Monte Carlo, suffer from exponentially diverging correlations in trajectory space as a function of the bias parameter when estimating large deviation functions. Improving the efficiencies of these algorithms requires introducing guiding functions for the trajectories.

  5. Importance sampling large deviations in nonequilibrium steady states. I

    NASA Astrophysics Data System (ADS)

    Ray, Ushnish; Chan, Garnet Kin-Lic; Limmer, David T.

    2018-03-01

    Large deviation functions contain information on the stability and response of systems driven into nonequilibrium steady states and in such a way are similar to free energies for systems at equilibrium. As with equilibrium free energies, evaluating large deviation functions numerically for all but the simplest systems is difficult because by construction they depend on exponentially rare events. In this first paper of a series, we evaluate different trajectory-based sampling methods capable of computing large deviation functions of time integrated observables within nonequilibrium steady states. We illustrate some convergence criteria and best practices using a number of different models, including a biased Brownian walker, a driven lattice gas, and a model of self-assembly. We show how two popular methods for sampling trajectory ensembles, transition path sampling and diffusion Monte Carlo, suffer from exponentially diverging correlations in trajectory space as a function of the bias parameter when estimating large deviation functions. Improving the efficiencies of these algorithms requires introducing guiding functions for the trajectories.

  6. Comparison of individual and pooled sampling methods for detecting bacterial pathogens of fish

    USGS Publications Warehouse

    Mumford, Sonia; Patterson, Chris; Evered, J.; Brunson, Ray; Levine, J.; Winton, J.

    2005-01-01

    Examination of finfish populations for viral and bacterial pathogens is an important component of fish disease control programs worldwide. Two methods are commonly used for collecting tissue samples for bacteriological culture, the currently accepted standards for detection of bacterial fish pathogens. The method specified in the Office International des Epizooties Manual of Diagnostic Tests for Aquatic Animals permits combining renal and splenic tissues from as many as 5 fish into pooled samples. The American Fisheries Society (AFS) Blue Book/US Fish and Wildlife Service (USFWS) Inspection Manual specifies the use of a bacteriological loop for collecting samples from the kidney of individual fish. An alternative would be to more fully utilize the pooled samples taken for virology. If implemented, this approach would provide substantial savings in labor and materials. To compare the relative performance of the AFS/USFWS method and this alternative approach, cultures of Yersinia ruckeri were used to establish low-level infections in groups of rainbow trout (Oncorhynchus mykiss) that were sampled by both methods. Yersinia ruckeri was cultured from 22 of 37 groups by at least 1 method. The loop method yielded 18 positive groups, with 1 group positive in the loop samples but negative in the pooled samples. The pooled samples produced 21 positive groups, with 4 groups positive in the pooled samples but negative in the loop samples. There was statistically significant agreement (Spearman coefficient 0.80, P < 0.001) in the relative ability of the 2 sampling methods to permit detection of low-level bacterial infections of rainbow trout.

  7. Standard methods for sampling freshwater fishes: Opportunities for international collaboration

    USGS Publications Warehouse

    Bonar, Scott A.; Mercado-Silva, Norman; Hubert, Wayne A.; Beard, Douglas; Dave, Göran; Kubečka, Jan; Graeb, Brian D. S.; Lester, Nigel P.; Porath, Mark T.; Winfield, Ian J.

    2017-01-01

    With publication of Standard Methods for Sampling North American Freshwater Fishes in 2009, the American Fisheries Society (AFS) recommended standard procedures for North America. To explore interest in standardizing at intercontinental scales, a symposium attended by international specialists in freshwater fish sampling was convened at the 145th Annual AFS Meeting in Portland, Oregon, in August 2015. Participants represented all continents except Australia and Antarctica and were employed by state and federal agencies, universities, nongovernmental organizations, and consulting businesses. Currently, standardization is practiced mostly in North America and Europe. Participants described how standardization has been important for management of long-term data sets, promoting fundamental scientific understanding, and assessing efficacy of large spatial scale management strategies. Academics indicated that standardization has been useful in fisheries education because time previously used to teach how sampling methods are developed is now more devoted to diagnosis and treatment of problem fish communities. Researchers reported that standardization allowed increased sample size for method validation and calibration. Group consensus was to retain continental standards where they currently exist but to further explore international and intercontinental standardization, specifically identifying where synergies and bridges exist, and identify means to collaborate with scientists where standardization is limited but interest and need occur.

  8. Development of an automated data processing method for sample to sample comparison of seized methamphetamines.

    PubMed

    Choe, Sanggil; Lee, Jaesin; Choi, Hyeyoung; Park, Yujin; Lee, Heesang; Pyo, Jaesung; Jo, Jiyeong; Park, Yonghoon; Choi, Hwakyung; Kim, Suncheun

    2012-11-30

    The information about the sources of supply, trafficking routes, distribution patterns and conspiracy links can be obtained from methamphetamine profiling. The precursor and synthetic method for the clandestine manufacture can be estimated from the analysis of minor impurities contained in methamphetamine. Also, the similarity between samples can be evaluated using the peaks that appear in chromatograms. In South Korea, methamphetamine was the most popular drug but the total seized amount of methamphetamine whole through the country was very small. Therefore, it would be more important to find the links between samples than the other uses of methamphetamine profiling. Many Asian countries including Japan and South Korea have been using the method developed by National Research Institute of Police Science of Japan. The method used gas chromatography-flame ionization detector (GC-FID), DB-5 column and four internal standards. It was developed to increase the amount of impurities and minimize the amount of methamphetamine. After GC-FID analysis, the raw data have to be processed. The data processing steps are very complex and require a lot of time and effort. In this study, Microsoft Visual Basic Application (VBA) modules were developed to handle these data processing steps. This module collected the results from the data into an Excel file and then corrected the retention time shift and response deviation generated from the sample preparation and instruments analysis. The developed modules were tested for their performance using 10 samples from 5 different cases. The processed results were analyzed with Pearson correlation coefficient for similarity assessment and the correlation coefficient of the two samples from the same case was more than 0.99. When the modules were applied to 131 seized methamphetamine samples, four samples from two different cases were found to have the common origin and the chromatograms of the four samples were appeared visually identical

  9. 19 CFR 151.83 - Method of sampling.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 19 Customs Duties 2 2010-04-01 2010-04-01 false Method of sampling. 151.83 Section 151.83 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Cotton § 151.83 Method of sampling. For...

  10. Sworn testimony of the model evidence: Gaussian Mixture Importance (GAME) sampling

    NASA Astrophysics Data System (ADS)

    Volpi, Elena; Schoups, Gerrit; Firmani, Giovanni; Vrugt, Jasper A.

    2017-07-01

    What is the "best" model? The answer to this question lies in part in the eyes of the beholder, nevertheless a good model must blend rigorous theory with redeeming qualities such as parsimony and quality of fit. Model selection is used to make inferences, via weighted averaging, from a set of K candidate models, Mk; k=>(1,…,K>), and help identify which model is most supported by the observed data, Y>˜=>(y˜1,…,y˜n>). Here, we introduce a new and robust estimator of the model evidence, p>(Y>˜|Mk>), which acts as normalizing constant in the denominator of Bayes' theorem and provides a single quantitative measure of relative support for each hypothesis that integrates model accuracy, uncertainty, and complexity. However, p>(Y>˜|Mk>) is analytically intractable for most practical modeling problems. Our method, coined GAussian Mixture importancE (GAME) sampling, uses bridge sampling of a mixture distribution fitted to samples of the posterior model parameter distribution derived from MCMC simulation. We benchmark the accuracy and reliability of GAME sampling by application to a diverse set of multivariate target distributions (up to 100 dimensions) with known values of p>(Y>˜|Mk>) and to hypothesis testing using numerical modeling of the rainfall-runoff transformation of the Leaf River watershed in Mississippi, USA. These case studies demonstrate that GAME sampling provides robust and unbiased estimates of the evidence at a relatively small computational cost outperforming commonly used estimators. The GAME sampler is implemented in the MATLAB package of DREAM and simplifies considerably scientific inquiry through hypothesis testing and model selection.

  11. Performance evaluation of an importance sampling technique in a Jackson network

    NASA Astrophysics Data System (ADS)

    brahim Mahdipour, E.; Masoud Rahmani, Amir; Setayeshi, Saeed

    2014-03-01

    Importance sampling is a technique that is commonly used to speed up Monte Carlo simulation of rare events. However, little is known regarding the design of efficient importance sampling algorithms in the context of queueing networks. The standard approach, which simulates the system using an a priori fixed change of measure suggested by large deviation analysis, has been shown to fail in even the simplest network settings. Estimating probabilities associated with rare events has been a topic of great importance in queueing theory, and in applied probability at large. In this article, we analyse the performance of an importance sampling estimator for a rare event probability in a Jackson network. This article carries out strict deadlines to a two-node Jackson network with feedback whose arrival and service rates are modulated by an exogenous finite state Markov process. We have estimated the probability of network blocking for various sets of parameters, and also the probability of missing the deadline of customers for different loads and deadlines. We have finally shown that the probability of total population overflow may be affected by various deadline values, service rates and arrival rates.

  12. [Wound microbial sampling methods in surgical practice, imprint techniques].

    PubMed

    Chovanec, Z; Veverková, L; Votava, M; Svoboda, J; Peštál, A; Doležel, J; Jedlička, V; Veselý, M; Wechsler, J; Čapov, I

    2012-12-01

    The wound is a damage of tissue. The process of healing is influenced by many systemic and local factors. The most crucial and the most discussed local factor of wound healing is infection. Surgical site infection in the wound is caused by micro-organisms. This information is known for many years, however the conditions leading to an infection occurrence have not been sufficiently described yet. Correct sampling technique, correct storage, transportation, evaluation, and valid interpretation of these data are very important in clinical practice. There are many methods for microbiological sampling, but the best one has not been yet identified and validated. We aim to discuss the problem with the focus on the imprint technique.

  13. Sampling bee communities using pan traps: alternative methods increase sample size

    USDA-ARS?s Scientific Manuscript database

    Monitoring of the status of bee populations and inventories of bee faunas require systematic sampling. Efficiency and ease of implementation has encouraged the use of pan traps to sample bees. Efforts to find an optimal standardized sampling method for pan traps have focused on pan trap color. Th...

  14. A Simple Sampling Method for Estimating the Accuracy of Large Scale Record Linkage Projects.

    PubMed

    Boyd, James H; Guiver, Tenniel; Randall, Sean M; Ferrante, Anna M; Semmens, James B; Anderson, Phil; Dickinson, Teresa

    2016-05-17

    Record linkage techniques allow different data collections to be brought together to provide a wider picture of the health status of individuals. Ensuring high linkage quality is important to guarantee the quality and integrity of research. Current methods for measuring linkage quality typically focus on precision (the proportion of incorrect links), given the difficulty of measuring the proportion of false negatives. The aim of this work is to introduce and evaluate a sampling based method to estimate both precision and recall following record linkage. In the sampling based method, record-pairs from each threshold (including those below the identified cut-off for acceptance) are sampled and clerically reviewed. These results are then applied to the entire set of record-pairs, providing estimates of false positives and false negatives. This method was evaluated on a synthetically generated dataset, where the true match status (which records belonged to the same person) was known. The sampled estimates of linkage quality were relatively close to actual linkage quality metrics calculated for the whole synthetic dataset. The precision and recall measures for seven reviewers were very consistent with little variation in the clerical assessment results (overall agreement using the Fleiss Kappa statistics was 0.601). This method presents as a possible means of accurately estimating matching quality and refining linkages in population level linkage studies. The sampling approach is especially important for large project linkages where the number of record pairs produced may be very large often running into millions.

  15. Detecting spatial structures in throughfall data: the effect of extent, sample size, sampling design, and variogram estimation method

    NASA Astrophysics Data System (ADS)

    Voss, Sebastian; Zimmermann, Beate; Zimmermann, Alexander

    2016-04-01

    In the last three decades, an increasing number of studies analyzed spatial patterns in throughfall to investigate the consequences of rainfall redistribution for biogeochemical and hydrological processes in forests. In the majority of cases, variograms were used to characterize the spatial properties of the throughfall data. The estimation of the variogram from sample data requires an appropriate sampling scheme: most importantly, a large sample and an appropriate layout of sampling locations that often has to serve both variogram estimation and geostatistical prediction. While some recommendations on these aspects exist, they focus on Gaussian data and high ratios of the variogram range to the extent of the study area. However, many hydrological data, and throughfall data in particular, do not follow a Gaussian distribution. In this study, we examined the effect of extent, sample size, sampling design, and calculation methods on variogram estimation of throughfall data. For our investigation, we first generated non-Gaussian random fields based on throughfall data with heavy outliers. Subsequently, we sampled the fields with three extents (plots with edge lengths of 25 m, 50 m, and 100 m), four common sampling designs (two grid-based layouts, transect and random sampling), and five sample sizes (50, 100, 150, 200, 400). We then estimated the variogram parameters by method-of-moments and residual maximum likelihood. Our key findings are threefold. First, the choice of the extent has a substantial influence on the estimation of the variogram. A comparatively small ratio of the extent to the correlation length is beneficial for variogram estimation. Second, a combination of a minimum sample size of 150, a design that ensures the sampling of small distances and variogram estimation by residual maximum likelihood offers a good compromise between accuracy and efficiency. Third, studies relying on method-of-moments based variogram estimation may have to employ at least

  16. An adaptive sampling method for variable-fidelity surrogate models using improved hierarchical kriging

    NASA Astrophysics Data System (ADS)

    Hu, Jiexiang; Zhou, Qi; Jiang, Ping; Shao, Xinyu; Xie, Tingli

    2018-01-01

    Variable-fidelity (VF) modelling methods have been widely used in complex engineering system design to mitigate the computational burden. Building a VF model generally includes two parts: design of experiments and metamodel construction. In this article, an adaptive sampling method based on improved hierarchical kriging (ASM-IHK) is proposed to refine the improved VF model. First, an improved hierarchical kriging model is developed as the metamodel, in which the low-fidelity model is varied through a polynomial response surface function to capture the characteristics of a high-fidelity model. Secondly, to reduce local approximation errors, an active learning strategy based on a sequential sampling method is introduced to make full use of the already required information on the current sampling points and to guide the sampling process of the high-fidelity model. Finally, two numerical examples and the modelling of the aerodynamic coefficient for an aircraft are provided to demonstrate the approximation capability of the proposed approach, as well as three other metamodelling methods and two sequential sampling methods. The results show that ASM-IHK provides a more accurate metamodel at the same simulation cost, which is very important in metamodel-based engineering design problems.

  17. Examination of Hydrate Formation Methods: Trying to Create Representative Samples

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kneafsey, T.J.; Rees, E.V.L.; Nakagawa, S.

    2011-04-01

    Forming representative gas hydrate-bearing laboratory samples is important so that the properties of these materials may be measured, while controlling the composition and other variables. Natural samples are rare, and have often experienced pressure and temperature changes that may affect the property to be measured [Waite et al., 2008]. Forming methane hydrate samples in the laboratory has been done a number of ways, each having advantages and disadvantages. The ice-to-hydrate method [Stern et al., 1996], contacts melting ice with methane at the appropriate pressure to form hydrate. The hydrate can then be crushed and mixed with mineral grains under controlledmore » conditions, and then compacted to create laboratory samples of methane hydrate in a mineral medium. The hydrate in these samples will be part of the load-bearing frame of the medium. In the excess gas method [Handa and Stupin, 1992], water is distributed throughout a mineral medium (e.g. packed moist sand, drained sand, moistened silica gel, other porous media) and the mixture is brought to hydrate-stable conditions (chilled and pressurized with gas), allowing hydrate to form. This method typically produces grain-cementing hydrate from pendular water in sand [Waite et al., 2004]. In the dissolved gas method [Tohidi et al., 2002], water with sufficient dissolved guest molecules is brought to hydrate-stable conditions where hydrate forms. In the laboratory, this is can be done by pre-dissolving the gas of interest in water and then introducing it to the sample under the appropriate conditions. With this method, it is easier to form hydrate from more soluble gases such as carbon dioxide. It is thought that this method more closely simulates the way most natural gas hydrate has formed. Laboratory implementation, however, is difficult, and sample formation is prohibitively time consuming [Minagawa et al., 2005; Spangenberg and Kulenkampff, 2005]. In another version of this technique, a specified quantity

  18. 7 CFR 58.812 - Methods of sample analysis.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Methods of sample analysis. 58.812 Section 58.812... Procedures § 58.812 Methods of sample analysis. Samples shall be tested according to the applicable methods of laboratory analysis contained in either DA Instruction 918-RL, as issued by the USDA, Agricultural...

  19. 7 CFR 58.245 - Method of sample analysis.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Method of sample analysis. 58.245 Section 58.245... Procedures § 58.245 Method of sample analysis. Samples shall be tested according to the applicable methods of laboratory analysis contained in either DA Instruction 918-RL as issued by the USDA, Agricultural Marketing...

  20. A nonparametric method to generate synthetic populations to adjust for complex sampling design features.

    PubMed

    Dong, Qi; Elliott, Michael R; Raghunathan, Trivellore E

    2014-06-01

    Outside of the survey sampling literature, samples are often assumed to be generated by a simple random sampling process that produces independent and identically distributed (IID) samples. Many statistical methods are developed largely in this IID world. Application of these methods to data from complex sample surveys without making allowance for the survey design features can lead to erroneous inferences. Hence, much time and effort have been devoted to develop the statistical methods to analyze complex survey data and account for the sample design. This issue is particularly important when generating synthetic populations using finite population Bayesian inference, as is often done in missing data or disclosure risk settings, or when combining data from multiple surveys. By extending previous work in finite population Bayesian bootstrap literature, we propose a method to generate synthetic populations from a posterior predictive distribution in a fashion inverts the complex sampling design features and generates simple random samples from a superpopulation point of view, making adjustment on the complex data so that they can be analyzed as simple random samples. We consider a simulation study with a stratified, clustered unequal-probability of selection sample design, and use the proposed nonparametric method to generate synthetic populations for the 2006 National Health Interview Survey (NHIS), and the Medical Expenditure Panel Survey (MEPS), which are stratified, clustered unequal-probability of selection sample designs.

  1. A nonparametric method to generate synthetic populations to adjust for complex sampling design features

    PubMed Central

    Dong, Qi; Elliott, Michael R.; Raghunathan, Trivellore E.

    2017-01-01

    Outside of the survey sampling literature, samples are often assumed to be generated by a simple random sampling process that produces independent and identically distributed (IID) samples. Many statistical methods are developed largely in this IID world. Application of these methods to data from complex sample surveys without making allowance for the survey design features can lead to erroneous inferences. Hence, much time and effort have been devoted to develop the statistical methods to analyze complex survey data and account for the sample design. This issue is particularly important when generating synthetic populations using finite population Bayesian inference, as is often done in missing data or disclosure risk settings, or when combining data from multiple surveys. By extending previous work in finite population Bayesian bootstrap literature, we propose a method to generate synthetic populations from a posterior predictive distribution in a fashion inverts the complex sampling design features and generates simple random samples from a superpopulation point of view, making adjustment on the complex data so that they can be analyzed as simple random samples. We consider a simulation study with a stratified, clustered unequal-probability of selection sample design, and use the proposed nonparametric method to generate synthetic populations for the 2006 National Health Interview Survey (NHIS), and the Medical Expenditure Panel Survey (MEPS), which are stratified, clustered unequal-probability of selection sample designs. PMID:29200608

  2. [Respondent-Driven Sampling: a new sampling method to study visible and hidden populations].

    PubMed

    Mantecón, Alejandro; Juan, Montse; Calafat, Amador; Becoña, Elisardo; Román, Encarna

    2008-01-01

    The paper introduces a variant of chain-referral sampling: respondent-driven sampling (RDS). This sampling method shows that methods based on network analysis can be combined with the statistical validity of standard probability sampling methods. In this sense, RDS appears to be a mathematical improvement of snowball sampling oriented to the study of hidden populations. However, we try to prove its validity with populations that are not within a sampling frame but can nonetheless be contacted without difficulty. The basics of RDS are explained through our research on young people (aged 14 to 25) who go clubbing, consume alcohol and other drugs, and have sex. Fieldwork was carried out between May and July 2007 in three Spanish regions: Baleares, Galicia and Comunidad Valenciana. The presentation of the study shows the utility of this type of sampling when the population is accessible but there is a difficulty deriving from the lack of a sampling frame. However, the sample obtained is not a random representative one in statistical terms of the target population. It must be acknowledged that the final sample is representative of a 'pseudo-population' that approximates to the target population but is not identical to it.

  3. Fluidics platform and method for sample preparation

    DOEpatents

    Benner, Henry W.; Dzenitis, John M.

    2016-06-21

    Provided herein are fluidics platforms and related methods for performing integrated sample collection and solid-phase extraction of a target component of the sample all in one tube. The fluidics platform comprises a pump, particles for solid-phase extraction and a particle-holding means. The method comprises contacting the sample with one or more reagents in a pump, coupling a particle-holding means to the pump and expelling the waste out of the pump while the particle-holding means retains the particles inside the pump. The fluidics platform and methods herein described allow solid-phase extraction without pipetting and centrifugation.

  4. Sampling methods for the study of pneumococcal carriage: a systematic review.

    PubMed

    Gladstone, R A; Jefferies, J M; Faust, S N; Clarke, S C

    2012-11-06

    Streptococcus pneumoniae is an important pathogen worldwide. Accurate sampling of S. pneumoniae carriage is central to surveillance studies before and following conjugate vaccination programmes to combat pneumococcal disease. Any bias introduced during sampling will affect downstream recovery and typing. Many variables exist for the method of collection and initial processing, which can make inter-laboratory or international comparisons of data complex. In February 2003, a World Health Organisation working group published a standard method for the detection of pneumococcal carriage for vaccine trials to reduce or eliminate variability. We sought to describe the variables associated with the sampling of S. pneumoniae from collection to storage in the context of the methods recommended by the WHO and those used in pneumococcal carriage studies since its publication. A search of published literature in the online PubMed database was performed on the 1st June 2012, to identify published studies that collected pneumococcal carriage isolates, conducted after the publication of the WHO standard method. After undertaking a systematic analysis of the literature, we show that a number of differences in pneumococcal sampling protocol continue to exist between studies since the WHO publication. The majority of studies sample from the nasopharynx, but the choice of swab and swab transport media is more variable between studies. At present there is insufficient experimental data that supports the optimal sensitivity of any standard method. This may have contributed to incomplete adoption of the primary stages of the WHO detection protocol, alongside pragmatic or logistical issues associated with study design. Consequently studies may not provide a true estimate of pneumococcal carriage. Optimal sampling of carriage could lead to improvements in downstream analysis and the evaluation of pneumococcal vaccine impact and extrapolation to pneumococcal disease control therefore

  5. New prior sampling methods for nested sampling - Development and testing

    NASA Astrophysics Data System (ADS)

    Stokes, Barrie; Tuyl, Frank; Hudson, Irene

    2017-06-01

    Nested Sampling is a powerful algorithm for fitting models to data in the Bayesian setting, introduced by Skilling [1]. The nested sampling algorithm proceeds by carrying out a series of compressive steps, involving successively nested iso-likelihood boundaries, starting with the full prior distribution of the problem parameters. The "central problem" of nested sampling is to draw at each step a sample from the prior distribution whose likelihood is greater than the current likelihood threshold, i.e., a sample falling inside the current likelihood-restricted region. For both flat and informative priors this ultimately requires uniform sampling restricted to the likelihood-restricted region. We present two new methods of carrying out this sampling step, and illustrate their use with the lighthouse problem [2], a bivariate likelihood used by Gregory [3] and a trivariate Gaussian mixture likelihood. All the algorithm development and testing reported here has been done with Mathematica® [4].

  6. Configurations and calibration methods for passive sampling techniques.

    PubMed

    Ouyang, Gangfeng; Pawliszyn, Janusz

    2007-10-19

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

  7. A Hybrid Monte Carlo importance sampling of rare events in Turbulence and in Turbulent Models

    NASA Astrophysics Data System (ADS)

    Margazoglou, Georgios; Biferale, Luca; Grauer, Rainer; Jansen, Karl; Mesterhazy, David; Rosenow, Tillmann; Tripiccione, Raffaele

    2017-11-01

    Extreme and rare events is a challenging topic in the field of turbulence. Trying to investigate those instances through the use of traditional numerical tools turns to be a notorious task, as they fail to systematically sample the fluctuations around them. On the other hand, we propose that an importance sampling Monte Carlo method can selectively highlight extreme events in remote areas of the phase space and induce their occurrence. We present a brand new computational approach, based on the path integral formulation of stochastic dynamics, and employ an accelerated Hybrid Monte Carlo (HMC) algorithm for this purpose. Through the paradigm of stochastic one-dimensional Burgers' equation, subjected to a random noise that is white-in-time and power-law correlated in Fourier space, we will prove our concept and benchmark our results with standard CFD methods. Furthermore, we will present our first results of constrained sampling around saddle-point instanton configurations (optimal fluctuations). The research leading to these results has received funding from the EU Horizon 2020 research and innovation programme under Grant Agreement No. 642069, and from the EU Seventh Framework Programme (FP7/2007-2013) under ERC Grant Agreement No. 339032.

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

    PubMed

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

    2015-06-01

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

  9. An adaptive importance sampling algorithm for Bayesian inversion with multimodal distributions

    DOE PAGES

    Li, Weixuan; Lin, Guang

    2015-03-21

    Parametric uncertainties are encountered in the simulations of many physical systems, and may be reduced by an inverse modeling procedure that calibrates the simulation results to observations on the real system being simulated. Following Bayes’ rule, a general approach for inverse modeling problems is to sample from the posterior distribution of the uncertain model parameters given the observations. However, the large number of repetitive forward simulations required in the sampling process could pose a prohibitive computational burden. This difficulty is particularly challenging when the posterior is multimodal. We present in this paper an adaptive importance sampling algorithm to tackle thesemore » challenges. Two essential ingredients of the algorithm are: 1) a Gaussian mixture (GM) model adaptively constructed as the proposal distribution to approximate the possibly multimodal target posterior, and 2) a mixture of polynomial chaos (PC) expansions, built according to the GM proposal, as a surrogate model to alleviate the computational burden caused by computational-demanding forward model evaluations. In three illustrative examples, the proposed adaptive importance sampling algorithm demonstrates its capabilities of automatically finding a GM proposal with an appropriate number of modes for the specific problem under study, and obtaining a sample accurately and efficiently representing the posterior with limited number of forward simulations.« less

  10. An adaptive importance sampling algorithm for Bayesian inversion with multimodal distributions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Li, Weixuan; Lin, Guang, E-mail: guanglin@purdue.edu

    2015-08-01

    Parametric uncertainties are encountered in the simulations of many physical systems, and may be reduced by an inverse modeling procedure that calibrates the simulation results to observations on the real system being simulated. Following Bayes' rule, a general approach for inverse modeling problems is to sample from the posterior distribution of the uncertain model parameters given the observations. However, the large number of repetitive forward simulations required in the sampling process could pose a prohibitive computational burden. This difficulty is particularly challenging when the posterior is multimodal. We present in this paper an adaptive importance sampling algorithm to tackle thesemore » challenges. Two essential ingredients of the algorithm are: 1) a Gaussian mixture (GM) model adaptively constructed as the proposal distribution to approximate the possibly multimodal target posterior, and 2) a mixture of polynomial chaos (PC) expansions, built according to the GM proposal, as a surrogate model to alleviate the computational burden caused by computational-demanding forward model evaluations. In three illustrative examples, the proposed adaptive importance sampling algorithm demonstrates its capabilities of automatically finding a GM proposal with an appropriate number of modes for the specific problem under study, and obtaining a sample accurately and efficiently representing the posterior with limited number of forward simulations.« less

  11. Differences in Movement Pattern and Detectability between Males and Females Influence How Common Sampling Methods Estimate Sex Ratio.

    PubMed

    Rodrigues, João Fabrício Mota; Coelho, Marco Túlio Pacheco

    2016-01-01

    Sampling the biodiversity is an essential step for conservation, and understanding the efficiency of sampling methods allows us to estimate the quality of our biodiversity data. Sex ratio is an important population characteristic, but until now, no study has evaluated how efficient are the sampling methods commonly used in biodiversity surveys in estimating the sex ratio of populations. We used a virtual ecologist approach to investigate whether active and passive capture methods are able to accurately sample a population's sex ratio and whether differences in movement pattern and detectability between males and females produce biased estimates of sex-ratios when using these methods. Our simulation allowed the recognition of individuals, similar to mark-recapture studies. We found that differences in both movement patterns and detectability between males and females produce biased estimates of sex ratios. However, increasing the sampling effort or the number of sampling days improves the ability of passive or active capture methods to properly sample sex ratio. Thus, prior knowledge regarding movement patterns and detectability for species is important information to guide field studies aiming to understand sex ratio related patterns.

  12. Differences in Movement Pattern and Detectability between Males and Females Influence How Common Sampling Methods Estimate Sex Ratio

    PubMed Central

    Rodrigues, João Fabrício Mota; Coelho, Marco Túlio Pacheco

    2016-01-01

    Sampling the biodiversity is an essential step for conservation, and understanding the efficiency of sampling methods allows us to estimate the quality of our biodiversity data. Sex ratio is an important population characteristic, but until now, no study has evaluated how efficient are the sampling methods commonly used in biodiversity surveys in estimating the sex ratio of populations. We used a virtual ecologist approach to investigate whether active and passive capture methods are able to accurately sample a population’s sex ratio and whether differences in movement pattern and detectability between males and females produce biased estimates of sex-ratios when using these methods. Our simulation allowed the recognition of individuals, similar to mark-recapture studies. We found that differences in both movement patterns and detectability between males and females produce biased estimates of sex ratios. However, increasing the sampling effort or the number of sampling days improves the ability of passive or active capture methods to properly sample sex ratio. Thus, prior knowledge regarding movement patterns and detectability for species is important information to guide field studies aiming to understand sex ratio related patterns. PMID:27441554

  13. Simulated Tempering Distributed Replica Sampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methods for Conformational Sampling.

    PubMed

    Rauscher, Sarah; Neale, Chris; Pomès, Régis

    2009-10-13

    Generalized-ensemble algorithms in temperature space have become popular tools to enhance conformational sampling in biomolecular simulations. A random walk in temperature leads to a corresponding random walk in potential energy, which can be used to cross over energetic barriers and overcome the problem of quasi-nonergodicity. In this paper, we introduce two novel methods: simulated tempering distributed replica sampling (STDR) and virtual replica exchange (VREX). These methods are designed to address the practical issues inherent in the replica exchange (RE), simulated tempering (ST), and serial replica exchange (SREM) algorithms. RE requires a large, dedicated, and homogeneous cluster of CPUs to function efficiently when applied to complex systems. ST and SREM both have the drawback of requiring extensive initial simulations, possibly adaptive, for the calculation of weight factors or potential energy distribution functions. STDR and VREX alleviate the need for lengthy initial simulations, and for synchronization and extensive communication between replicas. Both methods are therefore suitable for distributed or heterogeneous computing platforms. We perform an objective comparison of all five algorithms in terms of both implementation issues and sampling efficiency. We use disordered peptides in explicit water as test systems, for a total simulation time of over 42 μs. Efficiency is defined in terms of both structural convergence and temperature diffusion, and we show that these definitions of efficiency are in fact correlated. Importantly, we find that ST-based methods exhibit faster temperature diffusion and correspondingly faster convergence of structural properties compared to RE-based methods. Within the RE-based methods, VREX is superior to both SREM and RE. On the basis of our observations, we conclude that ST is ideal for simple systems, while STDR is well-suited for complex systems.

  14. An economic passive sampling method to detect particulate pollutants using magnetic measurements.

    PubMed

    Cao, Liwan; Appel, Erwin; Hu, Shouyun; Ma, Mingming

    2015-10-01

    Identifying particulate matter (PM) emitted from industrial processes into the atmosphere is an important issue in environmental research. This paper presents a passive sampling method using simple artificial samplers that maintains the advantage of bio-monitoring, but overcomes some of its disadvantages. The samplers were tested in a heavily polluted area (Linfen, China) and compared to results from leaf samples. Spatial variations of magnetic susceptibility from artificial passive samplers and leaf samples show very similar patterns. Scanning electron microscopy suggests that the collected PM are mostly in the range of 2-25 μm; frequent occurrence of spherical shape indicates industrial combustion dominates PM emission. Magnetic properties around power plants show different features than other plants. This sampling method provides a suitable and economic tool for semi-quantifying temporal and spatial distribution of air quality; they can be installed in a regular grid and calibrate the weight of PM. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Systems and methods for sample analysis

    DOEpatents

    Cooks, Robert Graham; Li, Guangtao; Li, Xin; Ouyang, Zheng

    2015-01-13

    The invention generally relates to systems and methods for sample analysis. In certain embodiments, the invention provides a system for analyzing a sample that includes a probe including a material connected to a high voltage source, a device for generating a heated gas, and a mass analyzer.

  16. Synchronization sampling method based on delta-sigma analog-digital converter for underwater towed array system.

    PubMed

    Jiang, Jia-Jia; Duan, Fa-Jie; Li, Yan-Chao; Hua, Xiang-Ning

    2014-03-01

    Synchronization sampling is very important in underwater towed array system where every acquisition node (AN) samples analog signals by its own analog-digital converter (ADC). In this paper, a simple and effective synchronization sampling method is proposed to ensure synchronized operation among different ANs of the underwater towed array system. We first present a master-slave synchronization sampling model, and then design a high accuracy phase-locked loop to synchronize all delta-sigma ADCs to a reference clock. However, when the master-slave synchronization sampling model is used, both the time-delay (TD) of messages traveling along the wired transmission medium and the jitter of the clocks will bring out synchronization sampling error (SSE). Therefore, a simple method is proposed to estimate and compensate the TD of the messages transmission, and then another effective method is presented to overcome the SSE caused by the jitter of the clocks. An experimental system with three ANs is set up, and the related experimental results verify the validity of the synchronization sampling method proposed in this paper.

  17. Synchronization sampling method based on delta-sigma analog-digital converter for underwater towed array system

    NASA Astrophysics Data System (ADS)

    Jiang, Jia-Jia; Duan, Fa-Jie; Li, Yan-Chao; Hua, Xiang-Ning

    2014-03-01

    Synchronization sampling is very important in underwater towed array system where every acquisition node (AN) samples analog signals by its own analog-digital converter (ADC). In this paper, a simple and effective synchronization sampling method is proposed to ensure synchronized operation among different ANs of the underwater towed array system. We first present a master-slave synchronization sampling model, and then design a high accuracy phase-locked loop to synchronize all delta-sigma ADCs to a reference clock. However, when the master-slave synchronization sampling model is used, both the time-delay (TD) of messages traveling along the wired transmission medium and the jitter of the clocks will bring out synchronization sampling error (SSE). Therefore, a simple method is proposed to estimate and compensate the TD of the messages transmission, and then another effective method is presented to overcome the SSE caused by the jitter of the clocks. An experimental system with three ANs is set up, and the related experimental results verify the validity of the synchronization sampling method proposed in this paper.

  18. Rapid fusion method for the determination of refractory thorium and uranium isotopes in soil samples

    DOE PAGES

    Maxwell, Sherrod L.; Hutchison, Jay B.; McAlister, Daniel R.

    2015-02-14

    Recently, approximately 80% of participating laboratories failed to accurately determine uranium isotopes in soil samples in the U.S Department of Energy Mixed Analyte Performance Evaluation Program (MAPEP) Session 30, due to incomplete dissolution of refractory particles in the samples. Failing laboratories employed acid dissolution methods, including hydrofluoric acid, to recover uranium from the soil matrix. The failures illustrate the importance of rugged soil dissolution methods for the accurate measurement of analytes in the sample matrix. A new rapid fusion method has been developed by the Savannah River National Laboratory (SRNL) to prepare 1-2 g soil sample aliquots very quickly, withmore » total dissolution of refractory particles. Soil samples are fused with sodium hydroxide at 600 ºC in zirconium crucibles to enable complete dissolution of the sample. Uranium and thorium are separated on stacked TEVA and TRU extraction chromatographic resin cartridges, prior to isotopic measurements by alpha spectrometry on cerium fluoride microprecipitation sources. Plutonium can also be separated and measured using this method. Batches of 12 samples can be prepared for measurement in <5 hours.« less

  19. Accounting for sampling patterns reverses the relative importance of trade and climate for the global sharing of exotic plants

    USGS Publications Warehouse

    Sofaer, Helen R.; Jarnevich, Catherine S.

    2017-01-01

    AimThe distributions of exotic species reflect patterns of human-mediated dispersal, species climatic tolerances and a suite of other biotic and abiotic factors. The relative importance of each of these factors will shape how the spread of exotic species is affected by ongoing economic globalization and climate change. However, patterns of trade may be correlated with variation in scientific sampling effort globally, potentially confounding studies that do not account for sampling patterns.LocationGlobal.Time periodMuseum records, generally from the 1800s up to 2015.Major taxa studiedPlant species exotic to the United States.MethodsWe used data from the Global Biodiversity Information Facility (GBIF) to summarize the number of plant species with exotic occurrences in the United States that also occur in each other country world-wide. We assessed the relative importance of trade and climatic similarity for explaining variation in the number of shared species while evaluating several methods to account for variation in sampling effort among countries.ResultsAccounting for variation in sampling effort reversed the relative importance of trade and climate for explaining numbers of shared species. Trade was strongly correlated with numbers of shared U.S. exotic plants between the United States and other countries before, but not after, accounting for sampling variation among countries. Conversely, accounting for sampling effort strengthened the relationship between climatic similarity and species sharing. Using the number of records as a measure of sampling effort provided a straightforward approach for the analysis of occurrence data, whereas species richness estimators and rarefaction were less effective at removing sampling bias.Main conclusionsOur work provides support for broad-scale climatic limitation on the distributions of exotic species, illustrates the need to account for variation in sampling effort in large biodiversity databases, and highlights the

  20. A new approach to importance sampling for the simulation of false alarms. [in radar systems

    NASA Technical Reports Server (NTRS)

    Lu, D.; Yao, K.

    1987-01-01

    In this paper a modified importance sampling technique for improving the convergence of Importance Sampling is given. By using this approach to estimate low false alarm rates in radar simulations, the number of Monte Carlo runs can be reduced significantly. For one-dimensional exponential, Weibull, and Rayleigh distributions, a uniformly minimum variance unbiased estimator is obtained. For Gaussian distribution the estimator in this approach is uniformly better than that of previously known Importance Sampling approach. For a cell averaging system, by combining this technique and group sampling, the reduction of Monte Carlo runs for a reference cell of 20 and false alarm rate of lE-6 is on the order of 170 as compared to the previously known Importance Sampling approach.

  1. Development of a novel cell sorting method that samples population diversity in flow cytometry.

    PubMed

    Osborne, Geoffrey W; Andersen, Stacey B; Battye, Francis L

    2015-11-01

    Flow cytometry based electrostatic cell sorting is an important tool in the separation of cell populations. Existing instruments can sort single cells into multi-well collection plates, and keep track of cell of origin and sorted well location. However currently single sorted cell results reflect the population distribution and fail to capture the population diversity. Software was designed that implements a novel sorting approach, "Slice and Dice Sorting," that links a graphical representation of a multi-well plate to logic that ensures that single cells are sampled and sorted from all areas defined by the sort region/s. Therefore the diversity of the total population is captured, and the more frequently occurring or rarer cell types are all sampled. The sorting approach was tested computationally, and using functional cell based assays. Computationally we demonstrate that conventional single cell sorting can sample as little as 50% of the population diversity dependant on the population distribution, and that Slice and Dice sorting samples much more of the variety present within a cell population. We then show by sorting single cells into wells using the Slice and Dice sorting method that there are cells sorted using this method that would be either rarely sorted, or not sorted at all using conventional single cell sorting approaches. The present study demonstrates a novel single cell sorting method that samples much more of the population diversity than current methods. It has implications in clonal selection, stem cell sorting, single cell sequencing and any areas where population heterogeneity is of importance. © 2015 International Society for Advancement of Cytometry.

  2. A sample preparation method for recovering suppressed analyte ions in MALDI TOF MS.

    PubMed

    Lou, Xianwen; de Waal, Bas F M; Milroy, Lech-Gustav; van Dongen, Joost L J

    2015-05-01

    In matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS), analyte signals can be substantially suppressed by other compounds in the sample. In this technical note, we describe a modified thin-layer sample preparation method that significantly reduces the analyte suppression effect (ASE). In our method, analytes are deposited on top of the surface of matrix preloaded on the MALDI plate. To prevent embedding of analyte into the matrix crystals, the sample solution were prepared without matrix and efforts were taken not to re-dissolve the preloaded matrix. The results with model mixtures of peptides, synthetic polymers and lipids show that detection of analyte ions, which were completely suppressed using the conventional dried-droplet method, could be effectively recovered by using our method. Our findings suggest that the incorporation of analytes in the matrix crystals has an important contributory effect on ASE. By reducing ASE, our method should be useful for the direct MALDI MS analysis of multicomponent mixtures. Copyright © 2015 John Wiley & Sons, Ltd.

  3. 40 CFR Appendix I to Part 261 - Representative Sampling Methods

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 25 2010-07-01 2010-07-01 false Representative Sampling Methods I...—Representative Sampling Methods The methods and equipment used for sampling waste materials will vary with the form and consistency of the waste materials to be sampled. Samples collected using the sampling...

  4. 40 CFR Appendix I to Part 261 - Representative Sampling Methods

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 26 2011-07-01 2011-07-01 false Representative Sampling Methods I...—Representative Sampling Methods The methods and equipment used for sampling waste materials will vary with the form and consistency of the waste materials to be sampled. Samples collected using the sampling...

  5. Evaluating Service Quality from Patients' Perceptions: Application of Importance-performance Analysis Method.

    PubMed

    Mohebifar, Rafat; Hasani, Hana; Barikani, Ameneh; Rafiei, Sima

    2016-08-01

    Providing high service quality is one of the main functions of health systems. Measuring service quality is the basic prerequisite for improving quality. The aim of this study was to evaluate the quality of service in teaching hospitals using importance-performance analysis matrix. A descriptive-analytic study was conducted through a cross-sectional method in six academic hospitals of Qazvin, Iran, in 2012. A total of 360 patients contributed to the study. The sampling technique was stratified random sampling. Required data were collected based on a standard questionnaire (SERVQUAL). Data analysis was done through SPSS version 18 statistical software and importance-performance analysis matrix. The results showed a significant gap between importance and performance in all five dimensions of service quality (p < 0.05). In reviewing the gap, "reliability" (2.36) and "assurance" (2.24) dimensions had the highest quality gap and "responsiveness" had the lowest gap (1.97). Also, according to findings, reliability and assurance were in Quadrant (I), empathy was in Quadrant (II), and tangibles and responsiveness were in Quadrant (IV) of the importance-performance matrix. The negative gap in all dimensions of quality shows that quality improvement is necessary in all dimensions. Using quality and diagnosis measurement instruments such as importance-performance analysis will help hospital managers with planning of service quality improvement and achieving long-term goals.

  6. Mixed Methods Sampling: A Typology with Examples

    ERIC Educational Resources Information Center

    Teddlie, Charles; Yu, Fen

    2007-01-01

    This article presents a discussion of mixed methods (MM) sampling techniques. MM sampling involves combining well-established qualitative and quantitative techniques in creative ways to answer research questions posed by MM research designs. Several issues germane to MM sampling are presented including the differences between probability and…

  7. Log sampling methods and software for stand and landscape analyses.

    Treesearch

    Lisa J. Bate; Torolf R. Torgersen; Michael J. Wisdom; Edward O. Garton; Shawn C. Clabough

    2008-01-01

    We describe methods for efficient, accurate sampling of logs at landscape and stand scales to estimate density, total length, cover, volume, and weight. Our methods focus on optimizing the sampling effort by choosing an appropriate sampling method and transect length for specific forest conditions and objectives. Sampling methods include the line-intersect method and...

  8. New methods for sampling sparse populations

    Treesearch

    Anna Ringvall

    2007-01-01

    To improve surveys of sparse objects, methods that use auxiliary information have been suggested. Guided transect sampling uses prior information, e.g., from aerial photographs, for the layout of survey strips. Instead of being laid out straight, the strips will wind between potentially more interesting areas. 3P sampling (probability proportional to prediction) uses...

  9. SOIL AND SEDIMENT SAMPLING METHODS

    EPA Science Inventory

    The EPA Office of Solid Waste and Emergency Response's (OSWER) Office of Superfund Remediation and Technology Innovation (OSRTI) needs innovative methods and techniques to solve new and difficult sampling and analytical problems found at the numerous Superfund sites throughout th...

  10. 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. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Modified electrokinetic sample injection method in chromatography and electrophoresis analysis

    DOEpatents

    Davidson, J. Courtney; Balch, Joseph W.

    2001-01-01

    A sample injection method for horizontal configured multiple chromatography or electrophoresis units, each containing a number of separation/analysis channels, that enables efficient introduction of analyte samples. This method for loading when taken in conjunction with horizontal microchannels allows much reduced sample volumes and a means of sample stacking to greatly reduce the concentration of the sample. This reduction in the amount of sample can lead to great cost savings in sample preparation, particularly in massively parallel applications such as DNA sequencing. The essence of this method is in preparation of the input of the separation channel, the physical sample introduction, and subsequent removal of excess material. By this method, sample volumes of 100 nanoliter to 2 microliters have been used successfully, compared to the typical 5 microliters of sample required by the prior separation/analysis method.

  12. Food and Feed Safety Assessment: The Importance of Proper Sampling.

    PubMed

    Kuiper, Harry A; Paoletti, Claudia

    2015-03-24

    The general principles for safety and nutritional evaluation of foods and feed and the potential health risks associated with hazardous compounds are described as developed by the Food and Agriculture Organization (FAO) and the World Health Organization (WHO) and further elaborated in the European Union-funded project Safe Foods. We underline the crucial role of sampling in foods/feed safety assessment. High quality sampling should always be applied to ensure the use of adequate and representative samples as test materials for hazard identification, toxicological and nutritional characterization of identified hazards, as well as for estimating quantitative and reliable exposure levels of foods/feed or related compounds of concern for humans and animals. The importance of representative sampling is emphasized through examples of risk analyses in different areas of foods/feed production. The Theory of Sampling (TOS) is recognized as the only framework within which to ensure accuracy and precision of all sampling steps involved in the field-to-fork continuum, which is crucial to monitor foods and feed safety. Therefore, TOS must be integrated in the well-established FAO/WHO risk assessment approach in order to guarantee a transparent and correct frame for the risk assessment and decision making process.

  13. Food and feed safety assessment: the importance of proper sampling.

    PubMed

    Kuiper, Harry A; Paoletti, Claudia

    2015-01-01

    The general principles for safety and nutritional evaluation of foods and feed and the potential health risks associated with hazardous compounds are described as developed by the Food and Agriculture Organization (FAO) and the World Health Organization (WHO) and further elaborated in the European Union-funded project Safe Foods. We underline the crucial role of sampling in foods/feed safety assessment. High quality sampling should always be applied to ensure the use of adequate and representative samples as test materials for hazard identification, toxicological and nutritional characterization of identified hazards, as well as for estimating quantitative and reliable exposure levels of foods/feed or related compounds of concern for humans and animals. The importance of representative sampling is emphasized through examples of risk analyses in different areas of foods/feed production. The Theory of Sampling (TOS) is recognized as the only framework within which to ensure accuracy and precision of all sampling steps involved in the field-to-fork continuum, which is crucial to monitor foods and feed safety. Therefore, TOS must be integrated in the well-established FAO/WHO risk assessment approach in order to guarantee a transparent and correct frame for the risk assessment and decision making process.

  14. Observational studies of patients in the emergency department: a comparison of 4 sampling methods.

    PubMed

    Valley, Morgan A; Heard, Kennon J; Ginde, Adit A; Lezotte, Dennis C; Lowenstein, Steven R

    2012-08-01

    We evaluate the ability of 4 sampling methods to generate representative samples of the emergency department (ED) population. We analyzed the electronic records of 21,662 consecutive patient visits at an urban, academic ED. From this population, we simulated different models of study recruitment in the ED by using 2 sample sizes (n=200 and n=400) and 4 sampling methods: true random, random 4-hour time blocks by exact sample size, random 4-hour time blocks by a predetermined number of blocks, and convenience or "business hours." For each method and sample size, we obtained 1,000 samples from the population. Using χ(2) tests, we measured the number of statistically significant differences between the sample and the population for 8 variables (age, sex, race/ethnicity, language, triage acuity, arrival mode, disposition, and payer source). Then, for each variable, method, and sample size, we compared the proportion of the 1,000 samples that differed from the overall ED population to the expected proportion (5%). Only the true random samples represented the population with respect to sex, race/ethnicity, triage acuity, mode of arrival, language, and payer source in at least 95% of the samples. Patient samples obtained using random 4-hour time blocks and business hours sampling systematically differed from the overall ED patient population for several important demographic and clinical variables. However, the magnitude of these differences was not large. Common sampling strategies selected for ED-based studies may affect parameter estimates for several representative population variables. However, the potential for bias for these variables appears small. Copyright © 2012. Published by Mosby, Inc.

  15. Improved importance sampling technique for efficient simulation of digital communication systems

    NASA Technical Reports Server (NTRS)

    Lu, Dingqing; Yao, Kung

    1988-01-01

    A new, improved importance sampling (IIS) approach to simulation is considered. Some basic concepts of IS are introduced, and detailed evolutions of simulation estimation variances for Monte Carlo (MC) and IS simulations are given. The general results obtained from these evolutions are applied to the specific previously known conventional importance sampling (CIS) technique and the new IIS technique. The derivation for a linear system with no signal random memory is considered in some detail. For the CIS technique, the optimum input scaling parameter is found, while for the IIS technique, the optimum translation parameter is found. The results are generalized to a linear system with memory and signals. Specific numerical and simulation results are given which show the advantages of CIS over MC and IIS over CIS for simulations of digital communications systems.

  16. Determination of methylmercury in marine biota samples with advanced mercury analyzer: method validation.

    PubMed

    Azemard, Sabine; Vassileva, Emilia

    2015-06-01

    In this paper, we present a simple, fast and cost-effective method for determination of methyl mercury (MeHg) in marine samples. All important parameters influencing the sample preparation process were investigated and optimized. Full validation of the method was performed in accordance to the ISO-17025 (ISO/IEC, 2005) and Eurachem guidelines. Blanks, selectivity, working range (0.09-3.0ng), recovery (92-108%), intermediate precision (1.7-4.5%), traceability, limit of detection (0.009ng), limit of quantification (0.045ng) and expanded uncertainty (15%, k=2) were assessed. Estimation of the uncertainty contribution of each parameter and the demonstration of traceability of measurement results was provided as well. Furthermore, the selectivity of the method was studied by analyzing the same sample extracts by advanced mercury analyzer (AMA) and gas chromatography-atomic fluorescence spectrometry (GC-AFS). Additional validation of the proposed procedure was effectuated by participation in the IAEA-461 worldwide inter-laboratory comparison exercises. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. Rapid method for sampling metals for materials identification

    NASA Technical Reports Server (NTRS)

    Higgins, L. E.

    1971-01-01

    Nondamaging process similar to electrochemical machining is useful in obtaining metal samples from places inaccessible to conventional sampling methods or where methods would be hazardous or contaminating to specimens. Process applies to industries where metals or metal alloys play a vital role.

  18. A structured sparse regression method for estimating isoform expression level from multi-sample RNA-seq data.

    PubMed

    Zhang, L; Liu, X J

    2016-06-03

    With the rapid development of next-generation high-throughput sequencing technology, RNA-seq has become a standard and important technique for transcriptome analysis. For multi-sample RNA-seq data, the existing expression estimation methods usually deal with each single-RNA-seq sample, and ignore that the read distributions are consistent across multiple samples. In the current study, we propose a structured sparse regression method, SSRSeq, to estimate isoform expression using multi-sample RNA-seq data. SSRSeq uses a non-parameter model to capture the general tendency of non-uniformity read distribution for all genes across multiple samples. Additionally, our method adds a structured sparse regularization, which not only incorporates the sparse specificity between a gene and its corresponding isoform expression levels, but also reduces the effects of noisy reads, especially for lowly expressed genes and isoforms. Four real datasets were used to evaluate our method on isoform expression estimation. Compared with other popular methods, SSRSeq reduced the variance between multiple samples, and produced more accurate isoform expression estimations, and thus more meaningful biological interpretations.

  19. Sampling of temporal networks: Methods and biases

    NASA Astrophysics Data System (ADS)

    Rocha, Luis E. C.; Masuda, Naoki; Holme, Petter

    2017-11-01

    Temporal networks have been increasingly used to model a diversity of systems that evolve in time; for example, human contact structures over which dynamic processes such as epidemics take place. A fundamental aspect of real-life networks is that they are sampled within temporal and spatial frames. Furthermore, one might wish to subsample networks to reduce their size for better visualization or to perform computationally intensive simulations. The sampling method may affect the network structure and thus caution is necessary to generalize results based on samples. In this paper, we study four sampling strategies applied to a variety of real-life temporal networks. We quantify the biases generated by each sampling strategy on a number of relevant statistics such as link activity, temporal paths and epidemic spread. We find that some biases are common in a variety of networks and statistics, but one strategy, uniform sampling of nodes, shows improved performance in most scenarios. Given the particularities of temporal network data and the variety of network structures, we recommend that the choice of sampling methods be problem oriented to minimize the potential biases for the specific research questions on hand. Our results help researchers to better design network data collection protocols and to understand the limitations of sampled temporal network data.

  20. A Method for Choosing the Best Samples for Mars Sample Return

    PubMed Central

    Gordon, Peter R.

    2018-01-01

    Abstract Success of a future Mars Sample Return mission will depend on the correct choice of samples. Pyrolysis-FTIR can be employed as a triage instrument for Mars Sample Return. The technique can thermally dissociate minerals and organic matter for detection. Identification of certain mineral types can determine the habitability of the depositional environment, past or present, while detection of organic matter may suggest past or present habitation. In Mars' history, the Theiikian era represents an attractive target for life search missions and the acquisition of samples. The acidic and increasingly dry Theiikian may have been habitable and followed a lengthy neutral and wet period in Mars' history during which life could have originated and proliferated to achieve relatively abundant levels of biomass with a wide distribution. Moreover, the sulfate minerals produced in the Theiikian are also known to be good preservers of organic matter. We have used pyrolysis-FTIR and samples from a Mars analog ferrous acid stream with a thriving ecosystem to test the triage concept. Pyrolysis-FTIR identified those samples with the greatest probability of habitability and habitation. A three-tier scoring system was developed based on the detection of (i) organic signals, (ii) carbon dioxide and water, and (iii) sulfur dioxide. The presence of each component was given a score of A, B, or C depending on whether the substance had been detected, tentatively detected, or not detected, respectively. Single-step (for greatest possible sensitivity) or multistep (for more diagnostic data) pyrolysis-FTIR methods informed the assignments. The system allowed the highest-priority samples to be categorized as AAA (or A*AA if the organic signal was complex), while the lowest-priority samples could be categorized as CCC. Our methods provide a mechanism with which to rank samples and identify those that should take the highest priority for return to Earth during a Mars Sample Return mission

  1. A Method for Choosing the Best Samples for Mars Sample Return.

    PubMed

    Gordon, Peter R; Sephton, Mark A

    2018-05-01

    Success of a future Mars Sample Return mission will depend on the correct choice of samples. Pyrolysis-FTIR can be employed as a triage instrument for Mars Sample Return. The technique can thermally dissociate minerals and organic matter for detection. Identification of certain mineral types can determine the habitability of the depositional environment, past or present, while detection of organic matter may suggest past or present habitation. In Mars' history, the Theiikian era represents an attractive target for life search missions and the acquisition of samples. The acidic and increasingly dry Theiikian may have been habitable and followed a lengthy neutral and wet period in Mars' history during which life could have originated and proliferated to achieve relatively abundant levels of biomass with a wide distribution. Moreover, the sulfate minerals produced in the Theiikian are also known to be good preservers of organic matter. We have used pyrolysis-FTIR and samples from a Mars analog ferrous acid stream with a thriving ecosystem to test the triage concept. Pyrolysis-FTIR identified those samples with the greatest probability of habitability and habitation. A three-tier scoring system was developed based on the detection of (i) organic signals, (ii) carbon dioxide and water, and (iii) sulfur dioxide. The presence of each component was given a score of A, B, or C depending on whether the substance had been detected, tentatively detected, or not detected, respectively. Single-step (for greatest possible sensitivity) or multistep (for more diagnostic data) pyrolysis-FTIR methods informed the assignments. The system allowed the highest-priority samples to be categorized as AAA (or A*AA if the organic signal was complex), while the lowest-priority samples could be categorized as CCC. Our methods provide a mechanism with which to rank samples and identify those that should take the highest priority for return to Earth during a Mars Sample Return mission. Key Words

  2. Appearance-based representative samples refining method for palmprint recognition

    NASA Astrophysics Data System (ADS)

    Wen, Jiajun; Chen, Yan

    2012-07-01

    The sparse representation can deal with the lack of sample problem due to utilizing of all the training samples. However, the discrimination ability will degrade when more training samples are used for representation. We propose a novel appearance-based palmprint recognition method. We aim to find a compromise between the discrimination ability and the lack of sample problem so as to obtain a proper representation scheme. Under the assumption that the test sample can be well represented by a linear combination of a certain number of training samples, we first select the representative training samples according to the contributions of the samples. Then we further refine the training samples by an iteration procedure, excluding the training sample with the least contribution to the test sample for each time. Experiments on PolyU multispectral palmprint database and two-dimensional and three-dimensional palmprint database show that the proposed method outperforms the conventional appearance-based palmprint recognition methods. Moreover, we also explore and find out the principle of the usage for the key parameters in the proposed algorithm, which facilitates to obtain high-recognition accuracy.

  3. Field Methods and Sample Collection Techniques for the Surveillance of West Nile Virus in Avian Hosts.

    PubMed

    Wheeler, Sarah S; Boyce, Walter M; Reisen, William K

    2016-01-01

    Avian hosts play an important role in the spread, maintenance, and amplification of West Nile virus (WNV). Avian susceptibility to WNV varies from species to species thus surveillance efforts can focus both on birds that survive infection and those that succumb. Here we describe methods for the collection and sampling of live birds for WNV antibodies or viremia, and methods for the sampling of dead birds. Target species and study design considerations are discussed.

  4. Real-Time PCR Method for Detection of Salmonella spp. in Environmental Samples.

    PubMed

    Kasturi, Kuppuswamy N; Drgon, Tomas

    2017-07-15

    The methods currently used for detecting Salmonella in environmental samples require 2 days to produce results and have limited sensitivity. Here, we describe the development and validation of a real-time PCR Salmonella screening method that produces results in 18 to 24 h. Primers and probes specific to the gene invA , group D, and Salmonella enterica serovar Enteritidis organisms were designed and evaluated for inclusivity and exclusivity using a panel of 329 Salmonella isolates representing 126 serovars and 22 non- Salmonella organisms. The invA - and group D-specific sets identified all the isolates accurately. The PCR method had 100% inclusivity and detected 1 to 2 copies of Salmonella DNA per reaction. Primers specific for Salmonella -differentiating fragment 1 (Sdf-1) in conjunction with the group D set had 100% inclusivity for 32 S Enteritidis isolates and 100% exclusivity for the 297 non-Enteritidis Salmonella isolates. Single-laboratory validation performed on 1,741 environmental samples demonstrated that the PCR method detected 55% more positives than the V itek i mmuno d iagnostic a ssay s ystem (VIDAS) method. The PCR results correlated well with the culture results, and the method did not report any false-negative results. The receiver operating characteristic (ROC) analysis documented excellent agreement between the results from the culture and PCR methods (area under the curve, 0.90; 95% confidence interval of 0.76 to 1.0) confirming the validity of the PCR method. IMPORTANCE This validated PCR method detects 55% more positives for Salmonella in half the time required for the reference method, VIDAS. The validated PCR method will help to strengthen public health efforts through rapid screening of Salmonella spp. in environmental samples.

  5. Real-Time PCR Method for Detection of Salmonella spp. in Environmental Samples

    PubMed Central

    Drgon, Tomas

    2017-01-01

    ABSTRACT The methods currently used for detecting Salmonella in environmental samples require 2 days to produce results and have limited sensitivity. Here, we describe the development and validation of a real-time PCR Salmonella screening method that produces results in 18 to 24 h. Primers and probes specific to the gene invA, group D, and Salmonella enterica serovar Enteritidis organisms were designed and evaluated for inclusivity and exclusivity using a panel of 329 Salmonella isolates representing 126 serovars and 22 non-Salmonella organisms. The invA- and group D-specific sets identified all the isolates accurately. The PCR method had 100% inclusivity and detected 1 to 2 copies of Salmonella DNA per reaction. Primers specific for Salmonella-differentiating fragment 1 (Sdf-1) in conjunction with the group D set had 100% inclusivity for 32 S. Enteritidis isolates and 100% exclusivity for the 297 non-Enteritidis Salmonella isolates. Single-laboratory validation performed on 1,741 environmental samples demonstrated that the PCR method detected 55% more positives than the Vitek immunodiagnostic assay system (VIDAS) method. The PCR results correlated well with the culture results, and the method did not report any false-negative results. The receiver operating characteristic (ROC) analysis documented excellent agreement between the results from the culture and PCR methods (area under the curve, 0.90; 95% confidence interval of 0.76 to 1.0) confirming the validity of the PCR method. IMPORTANCE This validated PCR method detects 55% more positives for Salmonella in half the time required for the reference method, VIDAS. The validated PCR method will help to strengthen public health efforts through rapid screening of Salmonella spp. in environmental samples. PMID:28500041

  6. Preparation of samples for leaf architecture studies, a method for mounting cleared leaves.

    PubMed

    Vasco, Alejandra; Thadeo, Marcela; Conover, Margaret; Daly, Douglas C

    2014-09-01

    Several recent waves of interest in leaf architecture have shown an expanding range of approaches and applications across a number of disciplines. Despite this increased interest, examination of existing archives of cleared and mounted leaves shows that current methods for mounting, in particular, yield unsatisfactory results and deterioration of samples over relatively short periods. Although techniques for clearing and staining leaves are numerous, published techniques for mounting leaves are scarce. • Here we present a complete protocol and recommendations for clearing, staining, and imaging leaves, and, most importantly, a method to permanently mount cleared leaves. • The mounting protocol is faster than other methods, inexpensive, and straightforward; moreover, it yields clear and permanent samples that can easily be imaged, scanned, and stored. Specimens mounted with this method preserve well, with leaves that were mounted more than 35 years ago showing no signs of bubbling or discoloration.

  7. A cryopreservation method for Pasteurella multocida from wetland samples

    USGS Publications Warehouse

    Moore, Melody K.; Shadduck, D.J.; Goldberg, Diana R.; Samuel, M.D.

    1998-01-01

    A cryopreservation method and improved isolation techniques for detection of Pasteurella multocida from wetland samples were developed. Wetland water samples were collected in the field, diluted in dimethyl sulfoxide (DMSO, final concentration 10%), and frozen at -180 C in a liquid nitrogen vapor shipper. Frozen samples were transported to the laboratory where they were subsequently thawed and processed in Pasteurella multocida selective broth (PMSB) to isolate P. multocida. This method allowed for consistent isolation of 2 to 18 organisms/ml from water seeded with known concentrations of P. multocida. The method compared favorably with the standard mouse inoculation method and allowed for preservation of the samples until they could be processed in the laboratory.

  8. Prevalence of Mixed-Methods Sampling Designs in Social Science Research

    ERIC Educational Resources Information Center

    Collins, Kathleen M. T.

    2006-01-01

    The purpose of this mixed-methods study was to document the prevalence of sampling designs utilised in mixed-methods research and to examine the interpretive consistency between interpretations made in mixed-methods studies and the sampling design used. Classification of studies was based on a two-dimensional mixed-methods sampling model. This…

  9. Interval sampling methods and measurement error: a computer simulation.

    PubMed

    Wirth, Oliver; Slaven, James; Taylor, Matthew A

    2014-01-01

    A simulation study was conducted to provide a more thorough account of measurement error associated with interval sampling methods. A computer program simulated the application of momentary time sampling, partial-interval recording, and whole-interval recording methods on target events randomly distributed across an observation period. The simulation yielded measures of error for multiple combinations of observation period, interval duration, event duration, and cumulative event duration. The simulations were conducted up to 100 times to yield measures of error variability. Although the present simulation confirmed some previously reported characteristics of interval sampling methods, it also revealed many new findings that pertain to each method's inherent strengths and weaknesses. The analysis and resulting error tables can help guide the selection of the most appropriate sampling method for observation-based behavioral assessments. © Society for the Experimental Analysis of Behavior.

  10. 40 CFR 80.335 - What gasoline sample retention requirements apply to refiners and importers?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 17 2013-07-01 2013-07-01 false What gasoline sample retention... PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Gasoline Sulfur Sampling, Testing and Retention Requirements for Refiners and Importers § 80.335 What gasoline sample...

  11. 40 CFR 80.335 - What gasoline sample retention requirements apply to refiners and importers?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 16 2010-07-01 2010-07-01 false What gasoline sample retention... PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Gasoline Sulfur Sampling, Testing and Retention Requirements for Refiners and Importers § 80.335 What gasoline sample...

  12. 40 CFR 80.335 - What gasoline sample retention requirements apply to refiners and importers?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 17 2012-07-01 2012-07-01 false What gasoline sample retention... PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Gasoline Sulfur Sampling, Testing and Retention Requirements for Refiners and Importers § 80.335 What gasoline sample...

  13. 40 CFR 80.335 - What gasoline sample retention requirements apply to refiners and importers?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 17 2014-07-01 2014-07-01 false What gasoline sample retention... PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Gasoline Sulfur Sampling, Testing and Retention Requirements for Refiners and Importers § 80.335 What gasoline sample...

  14. 40 CFR 80.335 - What gasoline sample retention requirements apply to refiners and importers?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 16 2011-07-01 2011-07-01 false What gasoline sample retention... PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) REGULATION OF FUELS AND FUEL ADDITIVES Gasoline Sulfur Sampling, Testing and Retention Requirements for Refiners and Importers § 80.335 What gasoline sample...

  15. An efficient and cost-effective method for preparing transmission electron microscopy samples from powders

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wen, Haiming; Lin, Yaojun; Seidman, David N.

    The preparation of transmission electron microcopy (TEM) samples from powders with particle sizes larger than ~100 nm poses a challenge. The existing methods are complicated and expensive, or have a low probability of success. Herein, we report a modified methodology for preparation of TEM samples from powders, which is efficient, cost-effective, and easy to perform. This method involves mixing powders with an epoxy on a piece of weighing paper, curing the powder–epoxy mixture to form a bulk material, grinding the bulk to obtain a thin foil, punching TEM discs from the foil, dimpling the discs, and ion milling the dimpledmore » discs to electron transparency. Compared with the well established and robust grinding–dimpling–ion-milling method for TEM sample preparation for bulk materials, our modified approach for preparing TEM samples from powders only requires two additional simple steps. In this article, step-by-step procedures for our methodology are described in detail, and important strategies to ensure success are elucidated. Furthermore, our methodology has been applied successfully for preparing TEM samples with large thin areas and high quality for many different mechanically milled metallic powders.« less

  16. An efficient and cost-effective method for preparing transmission electron microscopy samples from powders

    DOE PAGES

    Wen, Haiming; Lin, Yaojun; Seidman, David N.; ...

    2015-09-09

    The preparation of transmission electron microcopy (TEM) samples from powders with particle sizes larger than ~100 nm poses a challenge. The existing methods are complicated and expensive, or have a low probability of success. Herein, we report a modified methodology for preparation of TEM samples from powders, which is efficient, cost-effective, and easy to perform. This method involves mixing powders with an epoxy on a piece of weighing paper, curing the powder–epoxy mixture to form a bulk material, grinding the bulk to obtain a thin foil, punching TEM discs from the foil, dimpling the discs, and ion milling the dimpledmore » discs to electron transparency. Compared with the well established and robust grinding–dimpling–ion-milling method for TEM sample preparation for bulk materials, our modified approach for preparing TEM samples from powders only requires two additional simple steps. In this article, step-by-step procedures for our methodology are described in detail, and important strategies to ensure success are elucidated. Furthermore, our methodology has been applied successfully for preparing TEM samples with large thin areas and high quality for many different mechanically milled metallic powders.« less

  17. Evaluation of Two Surface Sampling Methods for Microbiological and Chemical Analyses To Assess the Presence of Biofilms in Food Companies.

    PubMed

    Maes, Sharon; Huu, Son Nguyen; Heyndrickx, Marc; Weyenberg, Stephanie van; Steenackers, Hans; Verplaetse, Alex; Vackier, Thijs; Sampers, Imca; Raes, Katleen; Reu, Koen De

    2017-12-01

    Biofilms are an important source of contamination in food companies, yet the composition of biofilms in practice is still mostly unknown. The chemical and microbiological characterization of surface samples taken after cleaning and disinfection is very important to distinguish free-living bacteria from the attached bacteria in biofilms. In this study, sampling methods that are potentially useful for both chemical and microbiological analyses of surface samples were evaluated. In the manufacturing facilities of eight Belgian food companies, surfaces were sampled after cleaning and disinfection using two sampling methods: the scraper-flocked swab method and the sponge stick method. Microbiological and chemical analyses were performed on these samples to evaluate the suitability of the sampling methods for the quantification of extracellular polymeric substance components and microorganisms originating from biofilms in these facilities. The scraper-flocked swab method was most suitable for chemical analyses of the samples because the material in these swabs did not interfere with determination of the chemical components. For microbiological enumerations, the sponge stick method was slightly but not significantly more effective than the scraper-flocked swab method. In all but one of the facilities, at least 20% of the sampled surfaces had more than 10 2 CFU/100 cm 2 . Proteins were found in 20% of the chemically analyzed surface samples, and carbohydrates and uronic acids were found in 15 and 8% of the samples, respectively. When chemical and microbiological results were combined, 17% of the sampled surfaces were contaminated with both microorganisms and at least one of the analyzed chemical components; thus, these surfaces were characterized as carrying biofilm. Overall, microbiological contamination in the food industry is highly variable by food sector and even within a facility at various sampling points and sampling times.

  18. Capillary microextraction: A new method for sampling methamphetamine vapour.

    PubMed

    Nair, M V; Miskelly, G M

    2016-11-01

    Clandestine laboratories pose a serious health risk to first responders, investigators, decontamination companies, and the public who may be inadvertently exposed to methamphetamine and other chemicals used in its manufacture. Therefore there is an urgent need for reliable methods to detect and measure methamphetamine at such sites. The most common method for determining methamphetamine contamination at former clandestine laboratory sites is selected surface wipe sampling, followed by analysis with gas chromatography-mass spectrometry (GC-MS). We are investigating the use of sampling for methamphetamine vapour to complement such wipe sampling. In this study, we report the use of capillary microextraction (CME) devices for sampling airborne methamphetamine, and compare their sampling efficiency with a previously reported dynamic SPME method. The CME devices consisted of PDMS-coated glass filter strips inside a glass tube. The devices were used to dynamically sample methamphetamine vapour in the range of 0.42-4.2μgm -3 , generated by a custom-built vapour dosing system, for 1-15min, and methamphetamine was analysed using a GC-MS fitted with a ChromatoProbe thermal desorption unit. The devices showed good reproducibility (RSD<15%), and a curvilinear pre-equilibrium relationship between sampling times and peak area, which can be utilised for calibration. Under identical sampling conditions, the CME devices were approximately 30 times more sensitive than the dynamic SPME method. The CME devices could be stored for up to 3days after sampling prior to analysis. Consecutive sampling of methamphetamine and its isotopic substitute, d-9 methamphetamine showed no competitive displacement. This suggests that CME devices, pre-loaded with an internal standard, could be a feasible method for sampling airborne methamphetamine at former clandestine laboratories. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  19. 40 CFR Appendix I to Part 261 - Representative Sampling Methods

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 27 2013-07-01 2013-07-01 false Representative Sampling Methods I Appendix I to Part 261 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) SOLID WASTES...—Representative Sampling Methods The methods and equipment used for sampling waste materials will vary with the...

  20. Magnetic Stirrer Method for the Detection of Trichinella Larvae in Muscle Samples.

    PubMed

    Mayer-Scholl, Anne; Pozio, Edoardo; Gayda, Jennifer; Thaben, Nora; Bahn, Peter; Nöckler, Karsten

    2017-03-03

    Trichinellosis is a debilitating disease in humans and is caused by the consumption of raw or undercooked meat of animals infected with the nematode larvae of the genus Trichinella. The most important sources of human infections worldwide are game meat and pork or pork products. In many countries, the prevention of human trichinellosis is based on the identification of infected animals by means of the artificial digestion of muscle samples from susceptible animal carcasses. There are several methods based on the digestion of meat but the magnetic stirrer method is considered the gold standard. This method allows the detection of Trichinella larvae by microscopy after the enzymatic digestion of muscle samples and subsequent filtration and sedimentation steps. Although this method does not require special and expensive equipment, internal controls cannot be used. Therefore, stringent quality management should be applied throughout the test. The aim of the present work is to provide detailed handling instructions and critical control points of the method to analysts, based on the experience of the European Union Reference Laboratory for Parasites and the National Reference Laboratory of Germany for Trichinella.

  1. Neutron activation analysis of certified samples by the absolute method

    NASA Astrophysics Data System (ADS)

    Kadem, F.; Belouadah, N.; Idiri, Z.

    2015-07-01

    The nuclear reactions analysis technique is mainly based on the relative method or the use of activation cross sections. In order to validate nuclear data for the calculated cross section evaluated from systematic studies, we used the neutron activation analysis technique (NAA) to determine the various constituent concentrations of certified samples for animal blood, milk and hay. In this analysis, the absolute method is used. The neutron activation technique involves irradiating the sample and subsequently performing a measurement of the activity of the sample. The fundamental equation of the activation connects several physical parameters including the cross section that is essential for the quantitative determination of the different elements composing the sample without resorting to the use of standard sample. Called the absolute method, it allows a measurement as accurate as the relative method. The results obtained by the absolute method showed that the values are as precise as the relative method requiring the use of standard sample for each element to be quantified.

  2. [Recent advances in sample preparation methods of plant hormones].

    PubMed

    Wu, Qian; Wang, Lus; Wu, Dapeng; Duan, Chunfeng; Guan, Yafeng

    2014-04-01

    Plant hormones are a group of naturally occurring trace substances which play a crucial role in controlling the plant development, growth and environment response. With the development of the chromatography and mass spectroscopy technique, chromatographic analytical method has become a widely used way for plant hormone analysis. Among the steps of chromatographic analysis, sample preparation is undoubtedly the most vital one. Thus, a highly selective and efficient sample preparation method is critical for accurate identification and quantification of phytohormones. For the three major kinds of plant hormones including acidic plant hormones & basic plant hormones, brassinosteroids and plant polypeptides, the sample preparation methods are reviewed in sequence especially the recently developed methods. The review includes novel methods, devices, extractive materials and derivative reagents for sample preparation of phytohormones analysis. Especially, some related works of our group are included. At last, the future developments in this field are also prospected.

  3. Sample Size Calculations for Population Size Estimation Studies Using Multiplier Methods With Respondent-Driven Sampling Surveys.

    PubMed

    Fearon, Elizabeth; Chabata, Sungai T; Thompson, Jennifer A; Cowan, Frances M; Hargreaves, James R

    2017-09-14

    While guidance exists for obtaining population size estimates using multiplier methods with respondent-driven sampling surveys, we lack specific guidance for making sample size decisions. To guide the design of multiplier method population size estimation studies using respondent-driven sampling surveys to reduce the random error around the estimate obtained. The population size estimate is obtained by dividing the number of individuals receiving a service or the number of unique objects distributed (M) by the proportion of individuals in a representative survey who report receipt of the service or object (P). We have developed an approach to sample size calculation, interpreting methods to estimate the variance around estimates obtained using multiplier methods in conjunction with research into design effects and respondent-driven sampling. We describe an application to estimate the number of female sex workers in Harare, Zimbabwe. There is high variance in estimates. Random error around the size estimate reflects uncertainty from M and P, particularly when the estimate of P in the respondent-driven sampling survey is low. As expected, sample size requirements are higher when the design effect of the survey is assumed to be greater. We suggest a method for investigating the effects of sample size on the precision of a population size estimate obtained using multipler methods and respondent-driven sampling. Uncertainty in the size estimate is high, particularly when P is small, so balancing against other potential sources of bias, we advise researchers to consider longer service attendance reference periods and to distribute more unique objects, which is likely to result in a higher estimate of P in the respondent-driven sampling survey. ©Elizabeth Fearon, Sungai T Chabata, Jennifer A Thompson, Frances M Cowan, James R Hargreaves. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 14.09.2017.

  4. Sediment sampling and processing methods in Hungary, and possible improvements

    NASA Astrophysics Data System (ADS)

    Tamas, Eniko Anna; Koch, Daniel; Varga, Gyorgy

    2016-04-01

    The importance of the monitoring of sediment processes is unquestionable: sediment balance of regulated rivers suffered substantial alterations in the past century, affecting navigation, energy production, fish habitats and floodplain ecosystems alike; infiltration times to our drinking water wells have shortened, exposing them to an eventual pollution event and making them vulnerable; and sediment-attached contaminants accumulate in floodplains and reservoirs, threatening our healthy environment. The changes in flood characteristics and rating curves of our rivers are regularly being researched and described, involving state-of-the-art measurement methods, modeling tools and traditional statistics. Sediment processes however, are much less known. Unlike the investigation of flow processes, sediment-related research is scarce, which is partly due to the outdated methodology and poor database background in the specific field. Sediment-related data, information and analyses form an important and integral part of Civil engineering in relation to rivers all over the world. In relation to the second largest river of Europe, the Danube, it is widely known in expert community and for long discussed at different expert forums that the sediment balance of the river Danube has changed drastically over the past century. Sediment monitoring on the river Danube started as early as the end of the 19th century, with scattered measurements carried out. Regular sediment sampling was developed in the first half of the 20th century all along the river, with different station density and monitoring frequencies in different countries. After the first few decades of regular sampling, the concept of (mainly industrial) development changed along the river and data needs changed as well, furthermore the complicated and inexact methods of sampling bed load on the alluvial reach of the river were not developed further. Frequency of suspended sediment sampling is very low along the river

  5. Methods in Enzymology: “Flexible backbone sampling methods to model and design protein alternative conformations”

    PubMed Central

    Ollikainen, Noah; Smith, Colin A.; Fraser, James S.; Kortemme, Tanja

    2013-01-01

    Sampling alternative conformations is key to understanding how proteins work and engineering them for new functions. However, accurately characterizing and modeling protein conformational ensembles remains experimentally and computationally challenging. These challenges must be met before protein conformational heterogeneity can be exploited in protein engineering and design. Here, as a stepping stone, we describe methods to detect alternative conformations in proteins and strategies to model these near-native conformational changes based on backrub-type Monte Carlo moves in Rosetta. We illustrate how Rosetta simulations that apply backrub moves improve modeling of point mutant side chain conformations, native side chain conformational heterogeneity, functional conformational changes, tolerated sequence space, protein interaction specificity, and amino acid co-variation across protein-protein interfaces. We include relevant Rosetta command lines and RosettaScripts to encourage the application of these types of simulations to other systems. Our work highlights that critical scoring and sampling improvements will be necessary to approximate conformational landscapes. Challenges for the future development of these methods include modeling conformational changes that propagate away from designed mutation sites and modulating backbone flexibility to predictively design functionally important conformational heterogeneity. PMID:23422426

  6. Method validation for control determination of mercury in fresh fish and shrimp samples by solid sampling thermal decomposition/amalgamation atomic absorption spectrometry.

    PubMed

    Torres, Daiane Placido; Martins-Teixeira, Maristela Braga; Cadore, Solange; Queiroz, Helena Müller

    2015-01-01

    A method for the determination of total mercury in fresh fish and shrimp samples by solid sampling thermal decomposition/amalgamation atomic absorption spectrometry (TDA AAS) has been validated following international foodstuff protocols in order to fulfill the Brazilian National Residue Control Plan. The experimental parameters have been previously studied and optimized according to specific legislation on validation and inorganic contaminants in foodstuff. Linearity, sensitivity, specificity, detection and quantification limits, precision (repeatability and within-laboratory reproducibility), robustness as well as accuracy of the method have been evaluated. Linearity of response was satisfactory for the two range concentrations available on the TDA AAS equipment, between approximately 25.0 and 200.0 μg kg(-1) (square regression) and 250.0 and 2000.0 μg kg(-1) (linear regression) of mercury. The residues for both ranges were homoscedastic and independent, with normal distribution. Correlation coefficients obtained for these ranges were higher than 0.995. Limits of quantification (LOQ) and of detection of the method (LDM), based on signal standard deviation (SD) for a low-in-mercury sample, were 3.0 and 1.0 μg kg(-1), respectively. Repeatability of the method was better than 4%. Within-laboratory reproducibility achieved a relative SD better than 6%. Robustness of the current method was evaluated and pointed sample mass as a significant factor. Accuracy (assessed as the analyte recovery) was calculated on basis of the repeatability, and ranged from 89% to 99%. The obtained results showed the suitability of the present method for direct mercury measurement in fresh fish and shrimp samples and the importance of monitoring the analysis conditions for food control purposes. Additionally, the competence of this method was recognized by accreditation under the standard ISO/IEC 17025.

  7. Salmonella spp. contamination in commercial layer hen farms using different types of samples and detection methods.

    PubMed

    Soria, M C; Soria, M A; Bueno, D J; Godano, E I; Gómez, S C; ViaButron, I A; Padin, V M; Rogé, A D

    2017-08-01

    The performance of detection methods (culture methods and polymerase chain reaction assay) and plating media used in the same type of samples were determined as well as the specificity of PCR primers to detected Salmonella spp. contamination in layer hen farms. Also, the association of farm characteristics with Salmonella presence was evaluated. Environmental samples (feces, feed, drinking water, air, boot-swabs) and eggs were taken from 40 layer hen houses. Salmonella spp. was most detected in boot-swabs taken around the houses (30% and 35% by isolation and PCR, respectively) follow by fecal samples (15.2% and 13.6% by isolation and PCR, respectively). Eggs, drinking water, and air samples were negative for Salmonella detection. Salmonella Schwarzengrund and S. Enteritidis were the most isolated serotypes. For plating media, relative specificity was 1, and the relative sensitivity was greater for EF-18 agar than XLDT agar in feed and fecal samples. However, relative sensitivity was greater in XLDT agar than EF-18 agar for boot-swab samples. Agreement was between fair to good depending on the sample, and it was good between isolation and PCR (feces and boot-swabs), without agreement for feed samples. Salmonella spp. PCR was positive for all strains, while S. Typhimurium PCR was negative. Salmonella Enteritidis PCR used was not specific. Based in the multiple logistic regression analyses, categorization by counties was significant for Salmonella spp. presence (P-value = 0.010). This study shows the importance of considering different types of samples, plating media and detection methods during a Salmonella spp. monitoring study. In addition, it is important to incorporate the sampling of floors around the layer hen houses to learn if biosecurity measures should be strengthened to minimize the entry and spread of Salmonella in the houses. Also, the performance of some PCR methods and S. Enteritidis PCR should be improved, and biosecurity measures in hen farms must be

  8. Photothermal method using a pyroelectric sensor for thermophysical characterization of agricultural and biological samples

    NASA Astrophysics Data System (ADS)

    Frandas, A.; Dadarlat, Dorin; Chirtoc, Mihai; Jalink, Henk; Bicanic, Dane D.; Paris, D.; Antoniow, Jean S.; Egee, Michel; Ungureanu, Costica

    1998-07-01

    The photopyroelectric method in different experimental configurations was used for thermophysical characterization of agricultural and biological samples. The study appears important due to the relation of thermal parameters to the quality of foodstuffs (connected to their preservation, storage and adulteration), migration profiles in biodegradable packages, and the mechanism of desiccation tolerance of seeds. Results are presented on the thermal parameters measurement and their dependence on temperature and water content for samples such as: honey, starch, seeds.

  9. Inferring the demographic history from DNA sequences: An importance sampling approach based on non-homogeneous processes.

    PubMed

    Ait Kaci Azzou, S; Larribe, F; Froda, S

    2016-10-01

    In Ait Kaci Azzou et al. (2015) we introduced an Importance Sampling (IS) approach for estimating the demographic history of a sample of DNA sequences, the skywis plot. More precisely, we proposed a new nonparametric estimate of a population size that changes over time. We showed on simulated data that the skywis plot can work well in typical situations where the effective population size does not undergo very steep changes. In this paper, we introduce an iterative procedure which extends the previous method and gives good estimates under such rapid variations. In the iterative calibrated skywis plot we approximate the effective population size by a piecewise constant function, whose values are re-estimated at each step. These piecewise constant functions are used to generate the waiting times of non homogeneous Poisson processes related to a coalescent process with mutation under a variable population size model. Moreover, the present IS procedure is based on a modified version of the Stephens and Donnelly (2000) proposal distribution. Finally, we apply the iterative calibrated skywis plot method to a simulated data set from a rapidly expanding exponential model, and we show that the method based on this new IS strategy correctly reconstructs the demographic history. Copyright © 2016. Published by Elsevier Inc.

  10. The Roche Immunoturbidimetric Albumin Method on Cobas c 501 Gives Higher Values Than the Abbott and Roche BCP Methods When Analyzing Patient Plasma Samples.

    PubMed

    Helmersson-Karlqvist, Johanna; Flodin, Mats; Havelka, Aleksandra Mandic; Xu, Xiao Yan; Larsson, Anders

    2016-09-01

    Serum/plasma albumin is an important and widely used laboratory marker and it is important that we measure albumin correctly without bias. We had indications that the immunoturbidimetric method on Cobas c 501 and the bromocresol purple (BCP) method on Architect 16000 differed, so we decided to study these methods more closely. A total of 1,951 patient requests with albumin measured with both the Architect BCP and Cobas immunoturbidimetric methods were extracted from the laboratory system. A comparison with fresh plasma samples was also performed that included immunoturbidimetric and BCP methods on Cobas c 501 and analysis of the international protein calibrator ERM-DA470k/IFCC. The median difference between the Abbott BCP and Roche immunoturbidimetric methods was 3.3 g/l and the Roche method overestimated ERM-DA470k/IFCC by 2.2 g/l. The Roche immunoturbidimetric method gave higher values than the Roche BCP method: y = 1.111x - 0.739, R² = 0.971. The Roche immunoturbidimetric albumin method gives clearly higher values than the Abbott and Roche BCP methods when analyzing fresh patient samples. The differences between the two methods were similar at normal and low albumin levels. © 2016 Wiley Periodicals, Inc.

  11. Survey of predators and sampling method comparison in sweet corn.

    PubMed

    Musser, Fred R; Nyrop, Jan P; Shelton, Anthony M

    2004-02-01

    Natural predation is an important component of integrated pest management that is often overlooked because it is difficult to quantify and perceived to be unreliable. To begin incorporating natural predation into sweet corn, Zea mays L., pest management, a predator survey was conducted and then three sampling methods were compared for their ability to accurately monitor the most abundant predators. A predator survey on sweet corn foliage in New York between 1999 and 2001 identified 13 species. Orius insidiosus (Say), Coleomegilla maculata (De Geer), and Harmonia axyridis (Pallas) were the most numerous predators in all years. To determine the best method for sampling adult and immature stages of these predators, comparisons were made among nondestructive field counts, destructive counts, and yellow sticky cards. Field counts were correlated with destructive counts for all populations, but field counts of small insects were biased. Sticky cards underrepresented immature populations. Yellow sticky cards were more attractive to C. maculata adults than H. axyridis adults, especially before pollen shed, making coccinellid population estimates based on sticky cards unreliable. Field counts were the most precise method for monitoring adult and immature stages of the three major predators. Future research on predicting predation of pests in sweet corn should be based on field counts of predators because these counts are accurate, have no associated supply costs, and can be made quickly.

  12. Preparation of samples for leaf architecture studies, a method for mounting cleared leaves1

    PubMed Central

    Vasco, Alejandra; Thadeo, Marcela; Conover, Margaret; Daly, Douglas C.

    2014-01-01

    • Premise of the study: Several recent waves of interest in leaf architecture have shown an expanding range of approaches and applications across a number of disciplines. Despite this increased interest, examination of existing archives of cleared and mounted leaves shows that current methods for mounting, in particular, yield unsatisfactory results and deterioration of samples over relatively short periods. Although techniques for clearing and staining leaves are numerous, published techniques for mounting leaves are scarce. • Methods and Results: Here we present a complete protocol and recommendations for clearing, staining, and imaging leaves, and, most importantly, a method to permanently mount cleared leaves. • Conclusions: The mounting protocol is faster than other methods, inexpensive, and straightforward; moreover, it yields clear and permanent samples that can easily be imaged, scanned, and stored. Specimens mounted with this method preserve well, with leaves that were mounted more than 35 years ago showing no signs of bubbling or discoloration. PMID:25225627

  13. Field evaluation of personal sampling methods for multiple bioaerosols.

    PubMed

    Wang, Chi-Hsun; Chen, Bean T; Han, Bor-Cheng; Liu, Andrew Chi-Yeu; Hung, Po-Chen; Chen, Chih-Yong; Chao, Hsing Jasmine

    2015-01-01

    Ambient bioaerosols are ubiquitous in the daily environment and can affect health in various ways. However, few studies have been conducted to comprehensively evaluate personal bioaerosol exposure in occupational and indoor environments because of the complex composition of bioaerosols and the lack of standardized sampling/analysis methods. We conducted a study to determine the most efficient collection/analysis method for the personal exposure assessment of multiple bioaerosols. The sampling efficiencies of three filters and four samplers were compared. According to our results, polycarbonate (PC) filters had the highest relative efficiency, particularly for bacteria. Side-by-side sampling was conducted to evaluate the three filter samplers (with PC filters) and the NIOSH Personal Bioaerosol Cyclone Sampler. According to the results, the Button Aerosol Sampler and the IOM Inhalable Dust Sampler had the highest relative efficiencies for fungi and bacteria, followed by the NIOSH sampler. Personal sampling was performed in a pig farm to assess occupational bioaerosol exposure and to evaluate the sampling/analysis methods. The Button and IOM samplers yielded a similar performance for personal bioaerosol sampling at the pig farm. However, the Button sampler is more likely to be clogged at high airborne dust concentrations because of its higher flow rate (4 L/min). Therefore, the IOM sampler is a more appropriate choice for performing personal sampling in environments with high dust levels. In summary, the Button and IOM samplers with PC filters are efficient sampling/analysis methods for the personal exposure assessment of multiple bioaerosols.

  14. Evaluating Composite Sampling Methods of Bacillus Spores at Low Concentrations

    PubMed Central

    Hess, Becky M.; Amidan, Brett G.; Anderson, Kevin K.; Hutchison, Janine R.

    2016-01-01

    Restoring all facility operations after the 2001 Amerithrax attacks took years to complete, highlighting the need to reduce remediation time. Some of the most time intensive tasks were environmental sampling and sample analyses. Composite sampling allows disparate samples to be combined, with only a single analysis needed, making it a promising method to reduce response times. We developed a statistical experimental design to test three different composite sampling methods: 1) single medium single pass composite (SM-SPC): a single cellulose sponge samples multiple coupons with a single pass across each coupon; 2) single medium multi-pass composite: a single cellulose sponge samples multiple coupons with multiple passes across each coupon (SM-MPC); and 3) multi-medium post-sample composite (MM-MPC): a single cellulose sponge samples a single surface, and then multiple sponges are combined during sample extraction. Five spore concentrations of Bacillus atrophaeus Nakamura spores were tested; concentrations ranged from 5 to 100 CFU/coupon (0.00775 to 0.155 CFU/cm2). Study variables included four clean surface materials (stainless steel, vinyl tile, ceramic tile, and painted dry wallboard) and three grime coated/dirty materials (stainless steel, vinyl tile, and ceramic tile). Analysis of variance for the clean study showed two significant factors: composite method (p< 0.0001) and coupon material (p = 0.0006). Recovery efficiency (RE) was higher overall using the MM-MPC method compared to the SM-SPC and SM-MPC methods. RE with the MM-MPC method for concentrations tested (10 to 100 CFU/coupon) was similar for ceramic tile, dry wall, and stainless steel for clean materials. RE was lowest for vinyl tile with both composite methods. Statistical tests for the dirty study showed RE was significantly higher for vinyl and stainless steel materials, but lower for ceramic tile. These results suggest post-sample compositing can be used to reduce sample analysis time when

  15. Evaluating Composite Sampling Methods of Bacillus Spores at Low Concentrations.

    PubMed

    Hess, Becky M; Amidan, Brett G; Anderson, Kevin K; Hutchison, Janine R

    2016-01-01

    Restoring all facility operations after the 2001 Amerithrax attacks took years to complete, highlighting the need to reduce remediation time. Some of the most time intensive tasks were environmental sampling and sample analyses. Composite sampling allows disparate samples to be combined, with only a single analysis needed, making it a promising method to reduce response times. We developed a statistical experimental design to test three different composite sampling methods: 1) single medium single pass composite (SM-SPC): a single cellulose sponge samples multiple coupons with a single pass across each coupon; 2) single medium multi-pass composite: a single cellulose sponge samples multiple coupons with multiple passes across each coupon (SM-MPC); and 3) multi-medium post-sample composite (MM-MPC): a single cellulose sponge samples a single surface, and then multiple sponges are combined during sample extraction. Five spore concentrations of Bacillus atrophaeus Nakamura spores were tested; concentrations ranged from 5 to 100 CFU/coupon (0.00775 to 0.155 CFU/cm2). Study variables included four clean surface materials (stainless steel, vinyl tile, ceramic tile, and painted dry wallboard) and three grime coated/dirty materials (stainless steel, vinyl tile, and ceramic tile). Analysis of variance for the clean study showed two significant factors: composite method (p< 0.0001) and coupon material (p = 0.0006). Recovery efficiency (RE) was higher overall using the MM-MPC method compared to the SM-SPC and SM-MPC methods. RE with the MM-MPC method for concentrations tested (10 to 100 CFU/coupon) was similar for ceramic tile, dry wall, and stainless steel for clean materials. RE was lowest for vinyl tile with both composite methods. Statistical tests for the dirty study showed RE was significantly higher for vinyl and stainless steel materials, but lower for ceramic tile. These results suggest post-sample compositing can be used to reduce sample analysis time when

  16. GROUND WATER PURGING AND SAMPLING METHODS: HISTORY VS. HYSTERIA

    EPA Science Inventory

    It has been over 10 years since the low-flow ground water purging and sampling method was initially reported in the literature. The method grew from the recognition that well purging was necessary to collect representative samples, bailers could not achieve well purging, and high...

  17. Approximation of the exponential integral (well function) using sampling methods

    NASA Astrophysics Data System (ADS)

    Baalousha, Husam Musa

    2015-04-01

    Exponential integral (also known as well function) is often used in hydrogeology to solve Theis and Hantush equations. Many methods have been developed to approximate the exponential integral. Most of these methods are based on numerical approximations and are valid for a certain range of the argument value. This paper presents a new approach to approximate the exponential integral. The new approach is based on sampling methods. Three different sampling methods; Latin Hypercube Sampling (LHS), Orthogonal Array (OA), and Orthogonal Array-based Latin Hypercube (OA-LH) have been used to approximate the function. Different argument values, covering a wide range, have been used. The results of sampling methods were compared with results obtained by Mathematica software, which was used as a benchmark. All three sampling methods converge to the result obtained by Mathematica, at different rates. It was found that the orthogonal array (OA) method has the fastest convergence rate compared with LHS and OA-LH. The root mean square error RMSE of OA was in the order of 1E-08. This method can be used with any argument value, and can be used to solve other integrals in hydrogeology such as the leaky aquifer integral.

  18. 9 CFR 327.11 - Receipts to importers for import product samples.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... product samples. 327.11 Section 327.11 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE... laboratory examination are to be used exclusively for that purpose, official receipts shall be issued and... collected, date of collection, and that the sample was collected for laboratory examination. The duplicate...

  19. Comparison of preprocessing methods and storage times for touch DNA samples

    PubMed Central

    Dong, Hui; Wang, Jing; Zhang, Tao; Ge, Jian-ye; Dong, Ying-qiang; Sun, Qi-fan; Liu, Chao; Li, Cai-xia

    2017-01-01

    Aim To select appropriate preprocessing methods for different substrates by comparing the effects of four different preprocessing methods on touch DNA samples and to determine the effect of various storage times on the results of touch DNA sample analysis. Method Hand touch DNA samples were used to investigate the detection and inspection results of DNA on different substrates. Four preprocessing methods, including the direct cutting method, stubbing procedure, double swab technique, and vacuum cleaner method, were used in this study. DNA was extracted from mock samples with four different preprocessing methods. The best preprocess protocol determined from the study was further used to compare performance after various storage times. DNA extracted from all samples was quantified and amplified using standard procedures. Results The amounts of DNA and the number of alleles detected on the porous substrates were greater than those on the non-porous substrates. The performances of the four preprocessing methods varied with different substrates. The direct cutting method displayed advantages for porous substrates, and the vacuum cleaner method was advantageous for non-porous substrates. No significant degradation trend was observed as the storage times increased. Conclusion Different substrates require the use of different preprocessing method in order to obtain the highest DNA amount and allele number from touch DNA samples. This study provides a theoretical basis for explorations of touch DNA samples and may be used as a reference when dealing with touch DNA samples in case work. PMID:28252870

  20. Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review.

    PubMed

    Fujisaki, Hiroshi; Moritsugu, Kei; Matsunaga, Yasuhiro; Morishita, Tetsuya; Maragliano, Luca

    2015-01-01

    Molecular Dynamics simulations are a powerful approach to study biomolecular conformational changes or protein-ligand, protein-protein, and protein-DNA/RNA interactions. Straightforward applications, however, are often hampered by incomplete sampling, since in a typical simulated trajectory the system will spend most of its time trapped by high energy barriers in restricted regions of the configuration space. Over the years, several techniques have been designed to overcome this problem and enhance space sampling. Here, we review a class of methods that rely on the idea of extending the set of dynamical variables of the system by adding extra ones associated to functions describing the process under study. In particular, we illustrate the Temperature Accelerated Molecular Dynamics (TAMD), Logarithmic Mean Force Dynamics (LogMFD), and Multiscale Enhanced Sampling (MSES) algorithms. We also discuss combinations with techniques for searching reaction paths. We show the advantages presented by this approach and how it allows to quickly sample important regions of the free-energy landscape via automatic exploration.

  1. Detection of enterotoxigenic Clostridium perfringens in meat samples by using molecular methods.

    PubMed

    Kaneko, Ikuko; Miyamoto, Kazuaki; Mimura, Kanako; Yumine, Natsuko; Utsunomiya, Hirotoshi; Akimoto, Shigeru; McClane, Bruce A

    2011-11-01

    To prevent food-borne bacterial diseases and to trace bacterial contamination events to foods, microbial source tracking (MST) methods provide important epidemiological information. To apply molecular methods to MST, it is necessary not only to amplify bacterial cells to detection limit levels but also to prepare DNA with reduced inhibitory compounds and contamination. Isolates carrying the Clostridium perfringens enterotoxin gene (cpe) on the chromosome or a plasmid rank among the most important food-borne pathogens. Previous surveys indicated that cpe-positive C. perfringens isolates are present in only ∼5% of nonoutbreak food samples and then only at low numbers, usually less than 3 cells/g. In this study, four molecular assays for the detection of cpe-positive C. perfringens isolates, i.e., ordinary PCR, nested PCR, real-time PCR, and loop-mediated isothermal amplification (LAMP), were developed and evaluated for their reliability using purified DNA. For use in the artificial contamination of meat samples, DNA templates were prepared by three different commercial DNA preparation kits. The four molecular assays always detected cpe when >10³ cells/g of cpe-positive C. perfringens were present, using any kit. Of three tested commercial DNA preparation kits, the InstaGene matrix kit appeared to be most suitable for the testing of a large number of samples. By using the InstaGene matrix kit, the four molecular assays efficiently detected cpe using DNA prepared from enrichment culture specimens of meat samples contaminated with low numbers of cpe-positive C. perfringens vegetative cells or spores. Overall, the current study developed molecular assay protocols for MST to detect the contamination of foods with low numbers of cells, and at a low frequency, of cpe-positive C. perfringens isolates.

  2. Evaluation of sampling methods for Bacillus spore-contaminated HVAC filters

    PubMed Central

    Calfee, M. Worth; Rose, Laura J.; Tufts, Jenia; Morse, Stephen; Clayton, Matt; Touati, Abderrahmane; Griffin-Gatchalian, Nicole; Slone, Christina; McSweeney, Neal

    2016-01-01

    The objective of this study was to compare an extraction-based sampling method to two vacuum-based sampling methods (vacuum sock and 37 mm cassette filter) with regards to their ability to recover Bacillus atrophaeus spores (surrogate for Bacillus anthracis) from pleated heating, ventilation, and air conditioning (HVAC) filters that are typically found in commercial and residential buildings. Electrostatic and mechanical HVAC filters were tested, both without and after loading with dust to 50% of their total holding capacity. The results were analyzed by one-way ANOVA across material types, presence or absence of dust, and sampling device. The extraction method gave higher relative recoveries than the two vacuum methods evaluated (p ≤ 0.001). On average, recoveries obtained by the vacuum methods were about 30% of those achieved by the extraction method. Relative recoveries between the two vacuum methods were not significantly different (p > 0.05). Although extraction methods yielded higher recoveries than vacuum methods, either HVAC filter sampling approach may provide a rapid and inexpensive mechanism for understanding the extent of contamination following a wide-area biological release incident. PMID:24184312

  3. 40 CFR 80.1644 - Sampling and testing requirements for producers and importers of certified ethanol denaturant.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... producers and importers of certified ethanol denaturant. 80.1644 Section 80.1644 Protection of Environment... ethanol denaturant. (a) Sample and test each batch of certified ethanol denaturant. (1) Producers and importers of certified ethanol denaturant shall collect a representative sample from each batch of certified...

  4. Systems and methods for self-synchronized digital sampling

    NASA Technical Reports Server (NTRS)

    Samson, Jr., John R. (Inventor)

    2008-01-01

    Systems and methods for self-synchronized data sampling are provided. In one embodiment, a system for capturing synchronous data samples is provided. The system includes an analog to digital converter adapted to capture signals from one or more sensors and convert the signals into a stream of digital data samples at a sampling frequency determined by a sampling control signal; and a synchronizer coupled to the analog to digital converter and adapted to receive a rotational frequency signal from a rotating machine, wherein the synchronizer is further adapted to generate the sampling control signal, and wherein the sampling control signal is based on the rotational frequency signal.

  5. Evaluating Composite Sampling Methods of Bacillus spores at Low Concentrations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hess, Becky M.; Amidan, Brett G.; Anderson, Kevin K.

    Restoring facility operations after the 2001 Amerithrax attacks took over three months to complete, highlighting the need to reduce remediation time. The most time intensive tasks were environmental sampling and sample analyses. Composite sampling allows disparate samples to be combined, with only a single analysis needed, making it a promising method to reduce response times. We developed a statistical experimental design to test three different composite sampling methods: 1) single medium single pass composite: a single cellulose sponge samples multiple coupons; 2) single medium multi-pass composite: a single cellulose sponge is used to sample multiple coupons; and 3) multi-medium post-samplemore » composite: a single cellulose sponge samples a single surface, and then multiple sponges are combined during sample extraction. Five spore concentrations of Bacillus atrophaeus Nakamura spores were tested; concentrations ranged from 5 to 100 CFU/coupon (0.00775 to 0.155CFU/cm2, respectively). Study variables included four clean surface materials (stainless steel, vinyl tile, ceramic tile, and painted wallboard) and three grime coated/dirty materials (stainless steel, vinyl tile, and ceramic tile). Analysis of variance for the clean study showed two significant factors: composite method (p-value < 0.0001) and coupon material (p-value = 0.0008). Recovery efficiency (RE) was higher overall using the post-sample composite (PSC) method compared to single medium composite from both clean and grime coated materials. RE with the PSC method for concentrations tested (10 to 100 CFU/coupon) was similar for ceramic tile, painted wall board, and stainless steel for clean materials. RE was lowest for vinyl tile with both composite methods. Statistical tests for the dirty study showed RE was significantly higher for vinyl and stainless steel materials, but significantly lower for ceramic tile. These results suggest post-sample compositing can be used to reduce sample analysis time

  6. Method and apparatus for sampling atmospheric mercury

    DOEpatents

    Trujillo, Patricio E.; Campbell, Evan E.; Eutsler, Bernard C.

    1976-01-20

    A method of simultaneously sampling particulate mercury, organic mercurial vapors, and metallic mercury vapor in the working and occupational environment and determining the amount of mercury derived from each such source in the sampled air. A known volume of air is passed through a sampling tube containing a filter for particulate mercury collection, a first adsorber for the selective adsorption of organic mercurial vapors, and a second adsorber for the adsorption of metallic mercury vapor. Carbon black molecular sieves are particularly useful as the selective adsorber for organic mercurial vapors. The amount of mercury adsorbed or collected in each section of the sampling tube is readily quantitatively determined by flameless atomic absorption spectrophotometry.

  7. Sampling pig farms at the abattoir in a cross-sectional study - Evaluation of a sampling method.

    PubMed

    Birkegård, Anna Camilla; Halasa, Tariq; Toft, Nils

    2017-09-15

    A cross-sectional study design is relatively inexpensive, fast and easy to conduct when compared to other study designs. Careful planning is essential to obtaining a representative sample of the population, and the recommended approach is to use simple random sampling from an exhaustive list of units in the target population. This approach is rarely feasible in practice, and other sampling procedures must often be adopted. For example, when slaughter pigs are the target population, sampling the pigs on the slaughter line may be an alternative to on-site sampling at a list of farms. However, it is difficult to sample a large number of farms from an exact predefined list, due to the logistics and workflow of an abattoir. Therefore, it is necessary to have a systematic sampling procedure and to evaluate the obtained sample with respect to the study objective. We propose a method for 1) planning, 2) conducting, and 3) evaluating the representativeness and reproducibility of a cross-sectional study when simple random sampling is not possible. We used an example of a cross-sectional study with the aim of quantifying the association of antimicrobial resistance and antimicrobial consumption in Danish slaughter pigs. It was not possible to visit farms within the designated timeframe. Therefore, it was decided to use convenience sampling at the abattoir. Our approach was carried out in three steps: 1) planning: using data from meat inspection to plan at which abattoirs and how many farms to sample; 2) conducting: sampling was carried out at five abattoirs; 3) evaluation: representativeness was evaluated by comparing sampled and non-sampled farms, and the reproducibility of the study was assessed through simulated sampling based on meat inspection data from the period where the actual data collection was carried out. In the cross-sectional study samples were taken from 681 Danish pig farms, during five weeks from February to March 2015. The evaluation showed that the sampling

  8. A New Automated Method and Sample Data Flow for Analysis of Volatile Nitrosamines in Human Urine*

    PubMed Central

    Hodgson, James A.; Seyler, Tiffany H.; McGahee, Ernest; Arnstein, Stephen; Wang, Lanqing

    2016-01-01

    Volatile nitrosamines (VNAs) are a group of compounds classified as probable (group 2A) and possible (group 2B) carcinogens in humans. Along with certain foods and contaminated drinking water, VNAs are detected at high levels in tobacco products and in both mainstream and sidestream smoke. Our laboratory monitors six urinary VNAs—N-nitrosodimethylamine (NDMA), N-nitrosomethylethylamine (NMEA), N-nitrosodiethylamine (NDEA), N-nitrosopiperidine (NPIP), N-nitrosopyrrolidine (NPYR), and N-nitrosomorpholine (NMOR)—using isotope dilution GC-MS/MS (QQQ) for large population studies such as the National Health and Nutrition Examination Survey (NHANES). In this paper, we report for the first time a new automated sample preparation method to more efficiently quantitate these VNAs. Automation is done using Hamilton STAR™ and Caliper Staccato™ workstations. This new automated method reduces sample preparation time from 4 hours to 2.5 hours while maintaining precision (inter-run CV < 10%) and accuracy (85% - 111%). More importantly this method increases sample throughput while maintaining a low limit of detection (<10 pg/mL) for all analytes. A streamlined sample data flow was created in parallel to the automated method, in which samples can be tracked from receiving to final LIMs output with minimal human intervention, further minimizing human error in the sample preparation process. This new automated method and the sample data flow are currently applied in bio-monitoring of VNAs in the US non-institutionalized population NHANES 2013-2014 cycle. PMID:26949569

  9. A field test of cut-off importance sampling for bole volume

    Treesearch

    Jeffrey H. Gove; Harry T. Valentine; Michael J. Holmes

    2000-01-01

    Cut-off importance sampling has recently been introduced as a technique for estimating bole volume to some point below the tree tip, termed the cut-off point. A field test of this technique was conducted on a small population of eastern white pine trees using dendrometry as the standard for volume estimation. Results showed that the differences in volume estimates...

  10. A Sequential Optimization Sampling Method for Metamodels with Radial Basis Functions

    PubMed Central

    Pan, Guang; Ye, Pengcheng; Yang, Zhidong

    2014-01-01

    Metamodels have been widely used in engineering design to facilitate analysis and optimization of complex systems that involve computationally expensive simulation programs. The accuracy of metamodels is strongly affected by the sampling methods. In this paper, a new sequential optimization sampling method is proposed. Based on the new sampling method, metamodels can be constructed repeatedly through the addition of sampling points, namely, extrema points of metamodels and minimum points of density function. Afterwards, the more accurate metamodels would be constructed by the procedure above. The validity and effectiveness of proposed sampling method are examined by studying typical numerical examples. PMID:25133206

  11. Evaluation of sampling methods for Bacillus spore-contaminated HVAC filters.

    PubMed

    Calfee, M Worth; Rose, Laura J; Tufts, Jenia; Morse, Stephen; Clayton, Matt; Touati, Abderrahmane; Griffin-Gatchalian, Nicole; Slone, Christina; McSweeney, Neal

    2014-01-01

    The objective of this study was to compare an extraction-based sampling method to two vacuum-based sampling methods (vacuum sock and 37mm cassette filter) with regards to their ability to recover Bacillus atrophaeus spores (surrogate for Bacillus anthracis) from pleated heating, ventilation, and air conditioning (HVAC) filters that are typically found in commercial and residential buildings. Electrostatic and mechanical HVAC filters were tested, both without and after loading with dust to 50% of their total holding capacity. The results were analyzed by one-way ANOVA across material types, presence or absence of dust, and sampling device. The extraction method gave higher relative recoveries than the two vacuum methods evaluated (p≤0.001). On average, recoveries obtained by the vacuum methods were about 30% of those achieved by the extraction method. Relative recoveries between the two vacuum methods were not significantly different (p>0.05). Although extraction methods yielded higher recoveries than vacuum methods, either HVAC filter sampling approach may provide a rapid and inexpensive mechanism for understanding the extent of contamination following a wide-area biological release incident. Published by Elsevier B.V.

  12. Methodology Series Module 5: Sampling Strategies.

    PubMed

    Setia, Maninder Singh

    2016-01-01

    Once the research question and the research design have been finalised, it is important to select the appropriate sample for the study. The method by which the researcher selects the sample is the ' Sampling Method'. There are essentially two types of sampling methods: 1) probability sampling - based on chance events (such as random numbers, flipping a coin etc.); and 2) non-probability sampling - based on researcher's choice, population that accessible & available. Some of the non-probability sampling methods are: purposive sampling, convenience sampling, or quota sampling. Random sampling method (such as simple random sample or stratified random sample) is a form of probability sampling. It is important to understand the different sampling methods used in clinical studies and mention this method clearly in the manuscript. The researcher should not misrepresent the sampling method in the manuscript (such as using the term ' random sample' when the researcher has used convenience sample). The sampling method will depend on the research question. For instance, the researcher may want to understand an issue in greater detail for one particular population rather than worry about the ' generalizability' of these results. In such a scenario, the researcher may want to use ' purposive sampling' for the study.

  13. An evaluation of long-term preservation methods for brown bear (Ursus arctos) faecal DNA samples

    USGS Publications Warehouse

    Murphy, M.A.; Waits, L.P.; Kendall, K.C.; Wasser, S.K.; Higbee, J.A.; Bogden, R.

    2002-01-01

    Relatively few large-scale faecal DNA studies have been initiated due to difficulties in amplifying low quality and quantity DNA template. To improve brown bear faecal DNA PCR amplification success rates and to determine post collection sample longevity, five preservation methods were evaluated: 90% ethanol, DETs buffer, silica-dried, oven-dried stored at room temperature, and oven-dried stored at -20??C. Preservation effectiveness was evaluated for 50 faecal samples by PCR amplification of a mitochondrial DNA (mtDNA) locus (???146 bp) and a nuclear DNA (nDNA) locus (???200 bp) at time points of one week, one month, three months and six months. Preservation method and storage time significantly impacted mtDNA and nDNA amplification success rates. For mtDNA, all preservation methods had ??? 75% success at one week, but storage time had a significant impact on the effectiveness of the silica preservation method. Ethanol preserved samples had the highest success rates for both mtDNA (86.5%) and nDNA (84%). Nuclear DNA amplification success rates ranged from 26-88%, and storage time had a significant impact on all methods but ethanol. Preservation method and storage time should be important considerations for researchers planning projects utilizing faecal DNA. We recommend preservation of faecal samples in 90% ethanol when feasible, although when collecting in remote field conditions or for both DNA and hormone assays a dry collection method may be advantageous.

  14. RAPID SEPARATION METHOD FOR EMERGENCY WATER AND URINE SAMPLES

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Maxwell, S.; Culligan, B.

    2008-08-27

    The Savannah River Site Environmental Bioassay Lab participated in the 2008 NRIP Emergency Response program administered by the National Institute for Standards and Technology (NIST) in May, 2008. A new rapid column separation method was used for analysis of actinides and {sup 90}Sr the NRIP 2008 emergency water and urine samples. Significant method improvements were applied to reduce analytical times. As a result, much faster analysis times were achieved, less than 3 hours for determination of {sup 90}Sr and 3-4 hours for actinides. This represents a 25%-33% improvement in analysis times from NRIP 2007 and a {approx}100% improvement compared tomore » NRIP 2006 report times. Column flow rates were increased by a factor of two, with no significant adverse impact on the method performance. Larger sample aliquots, shorter count times, faster cerium fluoride microprecipitation and streamlined calcium phosphate precipitation were also employed. Based on initial feedback from NIST, the SRS Environmental Bioassay Lab had the most rapid analysis times for actinides and {sup 90}Sr analyses for NRIP 2008 emergency urine samples. High levels of potential matrix interferences may be present in emergency samples and rugged methods are essential. Extremely high levels of {sup 210}Po were found to have an adverse effect on the uranium results for the NRIP-08 urine samples, while uranium results for NRIP-08 water samples were not affected. This problem, which was not observed for NRIP-06 or NRIP-07 urine samples, was resolved by using an enhanced {sup 210}Po removal step, which will be described.« less

  15. Importance Sampling in the Evaluation and Optimization of Buffered Failure Probability

    DTIC Science & Technology

    2015-07-01

    12th International Conference on Applications of Statistics and Probability in Civil Engineering, ICASP12 Vancouver, Canada, July 12-15, 2015...Importance Sampling in the Evaluation and Optimization of Buffered Failure Probability Marwan M. Harajli Graduate Student, Dept. of Civil and Environ...criterion is usually the failure probability . In this paper, we examine the buffered failure probability as an attractive alternative to the failure

  16. Sampling trace organic compounds in water: a comparison of a continuous active sampler to continuous passive and discrete sampling methods

    USGS Publications Warehouse

    Coes, Alissa L.; Paretti, Nicholas V.; Foreman, William T.; Iverson, Jana L.; Alvarez, David A.

    2014-01-01

    A continuous active sampling method was compared to continuous passive and discrete sampling methods for the sampling of trace organic compounds (TOCs) in water. Results from each method are compared and contrasted in order to provide information for future investigators to use while selecting appropriate sampling methods for their research. The continuous low-level aquatic monitoring (CLAM) sampler (C.I.Agent® Storm-Water Solutions) is a submersible, low flow-rate sampler, that continuously draws water through solid-phase extraction media. CLAM samplers were deployed at two wastewater-dominated stream field sites in conjunction with the deployment of polar organic chemical integrative samplers (POCIS) and the collection of discrete (grab) water samples. All samples were analyzed for a suite of 69 TOCs. The CLAM and POCIS samples represent time-integrated samples that accumulate the TOCs present in the water over the deployment period (19–23 h for CLAM and 29 days for POCIS); the discrete samples represent only the TOCs present in the water at the time and place of sampling. Non-metric multi-dimensional scaling and cluster analysis were used to examine patterns in both TOC detections and relative concentrations between the three sampling methods. A greater number of TOCs were detected in the CLAM samples than in corresponding discrete and POCIS samples, but TOC concentrations in the CLAM samples were significantly lower than in the discrete and (or) POCIS samples. Thirteen TOCs of varying polarity were detected by all of the three methods. TOC detections and concentrations obtained by the three sampling methods, however, are dependent on multiple factors. This study found that stream discharge, constituent loading, and compound type all affected TOC concentrations detected by each method. In addition, TOC detections and concentrations were affected by the reporting limits, bias, recovery, and performance of each method.

  17. Sampling trace organic compounds in water: a comparison of a continuous active sampler to continuous passive and discrete sampling methods.

    PubMed

    Coes, Alissa L; Paretti, Nicholas V; Foreman, William T; Iverson, Jana L; Alvarez, David A

    2014-03-01

    A continuous active sampling method was compared to continuous passive and discrete sampling methods for the sampling of trace organic compounds (TOCs) in water. Results from each method are compared and contrasted in order to provide information for future investigators to use while selecting appropriate sampling methods for their research. The continuous low-level aquatic monitoring (CLAM) sampler (C.I.Agent® Storm-Water Solutions) is a submersible, low flow-rate sampler, that continuously draws water through solid-phase extraction media. CLAM samplers were deployed at two wastewater-dominated stream field sites in conjunction with the deployment of polar organic chemical integrative samplers (POCIS) and the collection of discrete (grab) water samples. All samples were analyzed for a suite of 69 TOCs. The CLAM and POCIS samples represent time-integrated samples that accumulate the TOCs present in the water over the deployment period (19-23 h for CLAM and 29 days for POCIS); the discrete samples represent only the TOCs present in the water at the time and place of sampling. Non-metric multi-dimensional scaling and cluster analysis were used to examine patterns in both TOC detections and relative concentrations between the three sampling methods. A greater number of TOCs were detected in the CLAM samples than in corresponding discrete and POCIS samples, but TOC concentrations in the CLAM samples were significantly lower than in the discrete and (or) POCIS samples. Thirteen TOCs of varying polarity were detected by all of the three methods. TOC detections and concentrations obtained by the three sampling methods, however, are dependent on multiple factors. This study found that stream discharge, constituent loading, and compound type all affected TOC concentrations detected by each method. In addition, TOC detections and concentrations were affected by the reporting limits, bias, recovery, and performance of each method. Published by Elsevier B.V.

  18. Convenient mounting method for electrical measurements of thin samples

    NASA Technical Reports Server (NTRS)

    Matus, L. G.; Summers, R. L.

    1986-01-01

    A method for mounting thin samples for electrical measurements is described. The technique is based on a vacuum chuck concept in which the vacuum chuck simultaneously holds the sample and established electrical contact. The mounting plate is composed of a glass-ceramic insulating material and the surfaces of the plate and vacuum chuck are polished. The operation of the vacuum chuck is examined. The contacts on the sample and mounting plate, which are sputter-deposited through metal masks, are analyzed. The mounting method was utilized for van der Pauw measurements.

  19. Dynamic Method for Identifying Collected Sample Mass

    NASA Technical Reports Server (NTRS)

    Carson, John

    2008-01-01

    G-Sample is designed for sample collection missions to identify the presence and quantity of sample material gathered by spacecraft equipped with end effectors. The software method uses a maximum-likelihood estimator to identify the collected sample's mass based on onboard force-sensor measurements, thruster firings, and a dynamics model of the spacecraft. This makes sample mass identification a computation rather than a process requiring additional hardware. Simulation examples of G-Sample are provided for spacecraft model configurations with a sample collection device mounted on the end of an extended boom. In the absence of thrust knowledge errors, the results indicate that G-Sample can identify the amount of collected sample mass to within 10 grams (with 95-percent confidence) by using a force sensor with a noise and quantization floor of 50 micrometers. These results hold even in the presence of realistic parametric uncertainty in actual spacecraft inertia, center-of-mass offset, and first flexibility modes. Thrust profile knowledge is shown to be a dominant sensitivity for G-Sample, entering in a nearly one-to-one relationship with the final mass estimation error. This means thrust profiles should be well characterized with onboard accelerometers prior to sample collection. An overall sample-mass estimation error budget has been developed to approximate the effect of model uncertainty, sensor noise, data rate, and thrust profile error on the expected estimate of collected sample mass.

  20. GeoLab Concept: The Importance of Sample Selection During Long Duration Human Exploration Mission

    NASA Technical Reports Server (NTRS)

    Calaway, M. J.; Evans, C. A.; Bell, M. S.; Graff, T. G.

    2011-01-01

    In the future when humans explore planetary surfaces on the Moon, Mars, and asteroids or beyond, the return of geologic samples to Earth will be a high priority for human spaceflight operations. All future sample return missions will have strict down-mass and volume requirements; methods for in-situ sample assessment and prioritization will be critical for selecting the best samples for return-to-Earth.

  1. Methodology Series Module 5: Sampling Strategies

    PubMed Central

    Setia, Maninder Singh

    2016-01-01

    Once the research question and the research design have been finalised, it is important to select the appropriate sample for the study. The method by which the researcher selects the sample is the ‘ Sampling Method’. There are essentially two types of sampling methods: 1) probability sampling – based on chance events (such as random numbers, flipping a coin etc.); and 2) non-probability sampling – based on researcher's choice, population that accessible & available. Some of the non-probability sampling methods are: purposive sampling, convenience sampling, or quota sampling. Random sampling method (such as simple random sample or stratified random sample) is a form of probability sampling. It is important to understand the different sampling methods used in clinical studies and mention this method clearly in the manuscript. The researcher should not misrepresent the sampling method in the manuscript (such as using the term ‘ random sample’ when the researcher has used convenience sample). The sampling method will depend on the research question. For instance, the researcher may want to understand an issue in greater detail for one particular population rather than worry about the ‘ generalizability’ of these results. In such a scenario, the researcher may want to use ‘ purposive sampling’ for the study. PMID:27688438

  2. SOIL AND SEDIMENT SAMPLING METHODS | Science ...

    EPA Pesticide Factsheets

    The EPA Office of Solid Waste and Emergency Response's (OSWER) Office of Superfund Remediation and Technology Innovation (OSRTI) needs innovative methods and techniques to solve new and difficult sampling and analytical problems found at the numerous Superfund sites throughout the United States. Inadequate site characterization and a lack of knowledge of surface and subsurface contaminant distributions hinders EPA's ability to make the best decisions on remediation options and to conduct the most effective cleanup efforts. To assist OSWER, NERL conducts research to improve their capability to more accurately, precisely, and efficiently characterize Superfund, RCRA, LUST, oil spills, and brownfield sites and to improve their risk-based decision making capabilities, research is being conducted on improving soil and sediment sampling techniques and improving the sampling and handling of volatile organic compound (VOC) contaminated soils, among the many research programs and tasks being performed at ESD-LV.Under this task, improved sampling approaches and devices will be developed for characterizing the concentration of VOCs in soils. Current approaches and devices used today can lose up to 99% of the VOCs present in the sample due inherent weaknesses in the device and improper/inadequate collection techniques. This error generally causes decision makers to markedly underestimate the soil VOC concentrations and, therefore, to greatly underestimate the ecological

  3. Reliability of the Parabola Approximation Method in Heart Rate Variability Analysis Using Low-Sampling-Rate Photoplethysmography.

    PubMed

    Baek, Hyun Jae; Shin, JaeWook; Jin, Gunwoo; Cho, Jaegeol

    2017-10-24

    Photoplethysmographic signals are useful for heart rate variability analysis in practical ambulatory applications. While reducing the sampling rate of signals is an important consideration for modern wearable devices that enable 24/7 continuous monitoring, there have not been many studies that have investigated how to compensate the low timing resolution of low-sampling-rate signals for accurate heart rate variability analysis. In this study, we utilized the parabola approximation method and measured it against the conventional cubic spline interpolation method for the time, frequency, and nonlinear domain variables of heart rate variability. For each parameter, the intra-class correlation, standard error of measurement, Bland-Altman 95% limits of agreement and root mean squared relative error were presented. Also, elapsed time taken to compute each interpolation algorithm was investigated. The results indicated that parabola approximation is a simple, fast, and accurate algorithm-based method for compensating the low timing resolution of pulse beat intervals. In addition, the method showed comparable performance with the conventional cubic spline interpolation method. Even though the absolute value of the heart rate variability variables calculated using a signal sampled at 20 Hz were not exactly matched with those calculated using a reference signal sampled at 250 Hz, the parabola approximation method remains a good interpolation method for assessing trends in HRV measurements for low-power wearable applications.

  4. 19 CFR 151.67 - Sampling by importer.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Wool and Hair § 151.67 Sampling by... quantities from the packages of wool or hair designated for examination, provided the bales or bags are...

  5. 19 CFR 151.67 - Sampling by importer.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Wool and Hair § 151.67 Sampling by... quantities from the packages of wool or hair designated for examination, provided the bales or bags are...

  6. 19 CFR 151.67 - Sampling by importer.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Wool and Hair § 151.67 Sampling by... quantities from the packages of wool or hair designated for examination, provided the bales or bags are...

  7. 19 CFR 151.67 - Sampling by importer.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... TREASURY (CONTINUED) EXAMINATION, SAMPLING, AND TESTING OF MERCHANDISE Wool and Hair § 151.67 Sampling by... quantities from the packages of wool or hair designated for examination, provided the bales or bags are...

  8. Methods for collection and analysis of water samples

    USGS Publications Warehouse

    Rainwater, Frank Hays; Thatcher, Leland Lincoln

    1960-01-01

    This manual contains methods used by the U.S. Geological Survey to collect, preserve, and analyze water samples. Throughout, the emphasis is on obtaining analytical results that accurately describe the chemical composition of the water in situ. Among the topics discussed are selection of sampling sites, frequency of sampling, field equipment, preservatives and fixatives, analytical techniques of water analysis, and instruments. Seventy-seven laboratory and field procedures are given for determining fifty-three water properties.

  9. Nonclinical dose formulation analysis method validation and sample analysis.

    PubMed

    Whitmire, Monica Lee; Bryan, Peter; Henry, Teresa R; Holbrook, John; Lehmann, Paul; Mollitor, Thomas; Ohorodnik, Susan; Reed, David; Wietgrefe, Holly D

    2010-12-01

    Nonclinical dose formulation analysis methods are used to confirm test article concentration and homogeneity in formulations and determine formulation stability in support of regulated nonclinical studies. There is currently no regulatory guidance for nonclinical dose formulation analysis method validation or sample analysis. Regulatory guidance for the validation of analytical procedures has been developed for drug product/formulation testing; however, verification of the formulation concentrations falls under the framework of GLP regulations (not GMP). The only current related regulatory guidance is the bioanalytical guidance for method validation. The fundamental parameters for bioanalysis and formulation analysis validations that overlap include: recovery, accuracy, precision, specificity, selectivity, carryover, sensitivity, and stability. Divergence in bioanalytical and drug product validations typically center around the acceptance criteria used. As the dose formulation samples are not true "unknowns", the concept of quality control samples that cover the entire range of the standard curve serving as the indication for the confidence in the data generated from the "unknown" study samples may not always be necessary. Also, the standard bioanalytical acceptance criteria may not be directly applicable, especially when the determined concentration does not match the target concentration. This paper attempts to reconcile the different practices being performed in the community and to provide recommendations of best practices and proposed acceptance criteria for nonclinical dose formulation method validation and sample analysis.

  10. The importance of quality control in validating concentrations of contaminants of emerging concern in source and treated drinking water samples.

    PubMed

    Batt, Angela L; Furlong, Edward T; Mash, Heath E; Glassmeyer, Susan T; Kolpin, Dana W

    2017-02-01

    A national-scale survey of 247 contaminants of emerging concern (CECs), including organic and inorganic chemical compounds, and microbial contaminants, was conducted in source and treated drinking water samples from 25 treatment plants across the United States. Multiple methods were used to determine these CECs, including six analytical methods to measure 174 pharmaceuticals, personal care products, and pesticides. A three-component quality assurance/quality control (QA/QC) program was designed for the subset of 174 CECs which allowed us to assess and compare performances of the methods used. The three components included: 1) a common field QA/QC protocol and sample design, 2) individual investigator-developed method-specific QA/QC protocols, and 3) a suite of 46 method comparison analytes that were determined in two or more analytical methods. Overall method performance for the 174 organic chemical CECs was assessed by comparing spiked recoveries in reagent, source, and treated water over a two-year period. In addition to the 247 CECs reported in the larger drinking water study, another 48 pharmaceutical compounds measured did not consistently meet predetermined quality standards. Methodologies that did not seem suitable for these analytes are overviewed. The need to exclude analytes based on method performance demonstrates the importance of additional QA/QC protocols. Published by Elsevier B.V.

  11. Validated Test Method 5030C: Purge-and-Trap for Aqueous Samples

    EPA Pesticide Factsheets

    This method describes a purge-and-trap procedure for the analysis of volatile organic compoundsin aqueous samples & water miscible liquid samples. It also describes the analysis of high concentration soil and waste sample extracts prepared in Method 5035.

  12. Turbidity threshold sampling: Methods and instrumentation

    Treesearch

    Rand Eads; Jack Lewis

    2001-01-01

    Traditional methods for determining the frequency of suspended sediment sample collection often rely on measurements, such as water discharge, that are not well correlated to sediment concentration. Stream power is generally not a good predictor of sediment concentration for rivers that transport the bulk of their load as fines, due to the highly variable routing of...

  13. Towards robust and repeatable sampling methods in eDNA based studies.

    PubMed

    Dickie, Ian A; Boyer, Stephane; Buckley, Hannah; Duncan, Richard P; Gardner, Paul; Hogg, Ian D; Holdaway, Robert J; Lear, Gavin; Makiola, Andreas; Morales, Sergio E; Powell, Jeff R; Weaver, Louise

    2018-05-26

    DNA based techniques are increasingly used for measuring the biodiversity (species presence, identity, abundance and community composition) of terrestrial and aquatic ecosystems. While there are numerous reviews of molecular methods and bioinformatic steps, there has been little consideration of the methods used to collect samples upon which these later steps are based. This represents a critical knowledge gap, as methodologically sound field sampling is the foundation for subsequent analyses. We reviewed field sampling methods used for metabarcoding studies of both terrestrial and freshwater ecosystem biodiversity over a nearly three-year period (n = 75). We found that 95% (n = 71) of these studies used subjective sampling methods, inappropriate field methods, and/or failed to provide critical methodological information. It would be possible for researchers to replicate only 5% of the metabarcoding studies in our sample, a poorer level of reproducibility than for ecological studies in general. Our findings suggest greater attention to field sampling methods and reporting is necessary in eDNA-based studies of biodiversity to ensure robust outcomes and future reproducibility. Methods must be fully and accurately reported, and protocols developed that minimise subjectivity. Standardisation of sampling protocols would be one way to help to improve reproducibility, and have additional benefits in allowing compilation and comparison of data from across studies. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  14. COMPARISON OF MACROINVERTEBRATE SAMPLING METHODS FOR NONWADEABLE STREAMS

    EPA Science Inventory

    The bioassessment of nonwadeable streams in the United States is increasing, but methods for these systems are not as well developed as for wadeable streams. In this study, we compared six benthic macroinvertebrate field sampling methods for nonwadeable streams based on those us...

  15. Comparison of Collection Methods for Fecal Samples in Microbiome Studies

    PubMed Central

    Vogtmann, Emily; Chen, Jun; Amir, Amnon; Shi, Jianxin; Abnet, Christian C.; Nelson, Heidi; Knight, Rob; Chia, Nicholas; Sinha, Rashmi

    2017-01-01

    Prospective cohort studies are needed to assess the relationship between the fecal microbiome and human health and disease. To evaluate fecal collection methods, we determined technical reproducibility, stability at ambient temperature, and accuracy of 5 fecal collection methods (no additive, 95% ethanol, RNAlater Stabilization Solution, fecal occult blood test cards, and fecal immunochemical test tubes). Fifty-two healthy volunteers provided fecal samples at the Mayo Clinic in Rochester, Minnesota, in 2014. One set from each sample collection method was frozen immediately, and a second set was incubated at room temperature for 96 hours and then frozen. Intraclass correlation coefficients (ICCs) were calculated for the relative abundance of 3 phyla, 2 alpha diversity metrics, and 4 beta diversity metrics. Technical reproducibility was high, with ICCs for duplicate fecal samples between 0.64 and 1.00. Stability for most methods was generally high, although the ICCs were below 0.60 for 95% ethanol in metrics that were more sensitive to relative abundance. When compared with fecal samples that were frozen immediately, the ICCs were below 0.60 for the metrics that were sensitive to relative abundance; however, the remaining 2 alpha diversity and 3 beta diversity metrics were all relatively accurate, with ICCs above 0.60. In conclusion, all fecal sample collection methods appear relatively reproducible, stable, and accurate. Future studies could use these collection methods for microbiome analyses. PMID:27986704

  16. Measuring larval nematode contamination on cattle pastures: Comparing two herbage sampling methods.

    PubMed

    Verschave, S H; Levecke, B; Duchateau, L; Vercruysse, J; Charlier, J

    2015-06-15

    Assessing levels of pasture larval contamination is frequently used to study the population dynamics of the free-living stages of parasitic nematodes of livestock. Direct quantification of infective larvae (L3) on herbage is the most applied method to measure pasture larval contamination. However, herbage collection remains labour intensive and there is a lack of studies addressing the variation induced by the sampling method and the required sample size. The aim of this study was (1) to compare two different sampling methods in terms of pasture larval count results and time required to sample, (2) to assess the amount of variation in larval counts at the level of sample plot, pasture and season, respectively and (3) to calculate the required sample size to assess pasture larval contamination with a predefined precision using random plots across pasture. Eight young stock pastures of different commercial dairy herds were sampled in three consecutive seasons during the grazing season (spring, summer and autumn). On each pasture, herbage samples were collected through both a double-crossed W-transect with samples taken every 10 steps (method 1) and four random located plots of 0.16 m(2) with collection of all herbage within the plot (method 2). The average (± standard deviation (SD)) pasture larval contamination using sampling methods 1 and 2 was 325 (± 479) and 305 (± 444)L3/kg dry herbage (DH), respectively. Large discrepancies in pasture larval counts of the same pasture and season were often seen between methods, but no significant difference (P = 0.38) in larval counts between methods was found. Less time was required to collect samples with method 2. This difference in collection time between methods was most pronounced for pastures with a surface area larger than 1 ha. The variation in pasture larval counts from samples generated by random plot sampling was mainly due to the repeated measurements on the same pasture in the same season (residual variance

  17. Clustering Methods with Qualitative Data: A Mixed Methods Approach for Prevention Research with Small Samples

    PubMed Central

    Henry, David; Dymnicki, Allison B.; Mohatt, Nathaniel; Allen, James; Kelly, James G.

    2016-01-01

    Qualitative methods potentially add depth to prevention research, but can produce large amounts of complex data even with small samples. Studies conducted with culturally distinct samples often produce voluminous qualitative data, but may lack sufficient sample sizes for sophisticated quantitative analysis. Currently lacking in mixed methods research are methods allowing for more fully integrating qualitative and quantitative analysis techniques. Cluster analysis can be applied to coded qualitative data to clarify the findings of prevention studies by aiding efforts to reveal such things as the motives of participants for their actions and the reasons behind counterintuitive findings. By clustering groups of participants with similar profiles of codes in a quantitative analysis, cluster analysis can serve as a key component in mixed methods research. This article reports two studies. In the first study, we conduct simulations to test the accuracy of cluster assignment using three different clustering methods with binary data as produced when coding qualitative interviews. Results indicated that hierarchical clustering, K-Means clustering, and latent class analysis produced similar levels of accuracy with binary data, and that the accuracy of these methods did not decrease with samples as small as 50. Whereas the first study explores the feasibility of using common clustering methods with binary data, the second study provides a “real-world” example using data from a qualitative study of community leadership connected with a drug abuse prevention project. We discuss the implications of this approach for conducting prevention research, especially with small samples and culturally distinct communities. PMID:25946969

  18. Clustering Methods with Qualitative Data: a Mixed-Methods Approach for Prevention Research with Small Samples.

    PubMed

    Henry, David; Dymnicki, Allison B; Mohatt, Nathaniel; Allen, James; Kelly, James G

    2015-10-01

    Qualitative methods potentially add depth to prevention research but can produce large amounts of complex data even with small samples. Studies conducted with culturally distinct samples often produce voluminous qualitative data but may lack sufficient sample sizes for sophisticated quantitative analysis. Currently lacking in mixed-methods research are methods allowing for more fully integrating qualitative and quantitative analysis techniques. Cluster analysis can be applied to coded qualitative data to clarify the findings of prevention studies by aiding efforts to reveal such things as the motives of participants for their actions and the reasons behind counterintuitive findings. By clustering groups of participants with similar profiles of codes in a quantitative analysis, cluster analysis can serve as a key component in mixed-methods research. This article reports two studies. In the first study, we conduct simulations to test the accuracy of cluster assignment using three different clustering methods with binary data as produced when coding qualitative interviews. Results indicated that hierarchical clustering, K-means clustering, and latent class analysis produced similar levels of accuracy with binary data and that the accuracy of these methods did not decrease with samples as small as 50. Whereas the first study explores the feasibility of using common clustering methods with binary data, the second study provides a "real-world" example using data from a qualitative study of community leadership connected with a drug abuse prevention project. We discuss the implications of this approach for conducting prevention research, especially with small samples and culturally distinct communities.

  19. A comprehensive comparison of perpendicular distance sampling methods for sampling downed coarse woody debris

    Treesearch

    Jeffrey H. Gove; Mark J. Ducey; Harry T. Valentine; Michael S. Williams

    2013-01-01

    Many new methods for sampling down coarse woody debris have been proposed in the last dozen or so years. One of the most promising in terms of field application, perpendicular distance sampling (PDS), has several variants that have been progressively introduced in the literature. In this study, we provide an overview of the different PDS variants and comprehensive...

  20. A comparison of fitness-case sampling methods for genetic programming

    NASA Astrophysics Data System (ADS)

    Martínez, Yuliana; Naredo, Enrique; Trujillo, Leonardo; Legrand, Pierrick; López, Uriel

    2017-11-01

    Genetic programming (GP) is an evolutionary computation paradigm for automatic program induction. GP has produced impressive results but it still needs to overcome some practical limitations, particularly its high computational cost, overfitting and excessive code growth. Recently, many researchers have proposed fitness-case sampling methods to overcome some of these problems, with mixed results in several limited tests. This paper presents an extensive comparative study of four fitness-case sampling methods, namely: Interleaved Sampling, Random Interleaved Sampling, Lexicase Selection and Keep-Worst Interleaved Sampling. The algorithms are compared on 11 symbolic regression problems and 11 supervised classification problems, using 10 synthetic benchmarks and 12 real-world data-sets. They are evaluated based on test performance, overfitting and average program size, comparing them with a standard GP search. Comparisons are carried out using non-parametric multigroup tests and post hoc pairwise statistical tests. The experimental results suggest that fitness-case sampling methods are particularly useful for difficult real-world symbolic regression problems, improving performance, reducing overfitting and limiting code growth. On the other hand, it seems that fitness-case sampling cannot improve upon GP performance when considering supervised binary classification.

  1. Surface Sampling Collection and Culture Methods for Escherichia coli in Household Environments with High Fecal Contamination

    PubMed Central

    Kosek, Margaret N.; Schwab, Kellogg J.

    2017-01-01

    Empiric quantification of environmental fecal contamination is an important step toward understanding the impact that water, sanitation, and hygiene interventions have on reducing enteric infections. There is a need to standardize the methods used for surface sampling in field studies that examine fecal contamination in low-income settings. The dry cloth method presented in this manuscript improves upon the more commonly used swabbing technique that has been shown in the literature to have a low sampling efficiency. The recovery efficiency of a dry electrostatic cloth sampling method was evaluated using Escherichia coli and then applied to household surfaces in Iquitos, Peru, where there is high fecal contamination and enteric infection. Side-by-side measurements were taken from various floor locations within a household at the same time over a three-month period to compare for consistency of quantification of E. coli bacteria. The dry cloth sampling method in the laboratory setting showed 105% (95% Confidence Interval: 98%, 113%) E. coli recovery efficiency off of the cloths. The field application demonstrated strong agreement of side-by-side results (Pearson correlation coefficient for dirt surfaces was 0.83 (p < 0.0001) and 0.91 (p < 0.0001) for cement surfaces) and moderate agreement for results between entrance and kitchen samples (Pearson (0.53, p < 0.0001) and weighted Kappa statistic (0.54, p < 0.0001)). Our findings suggest that this method can be utilized in households with high bacterial loads using either continuous (quantitative) or categorical (semi-quantitative) data. The standardization of this low-cost, dry electrostatic cloth sampling method can be used to measure differences between households in intervention and non-intervention arms of randomized trials. PMID:28829392

  2. Surface Sampling Collection and Culture Methods for Escherichia coli in Household Environments with High Fecal Contamination.

    PubMed

    Exum, Natalie G; Kosek, Margaret N; Davis, Meghan F; Schwab, Kellogg J

    2017-08-22

    Empiric quantification of environmental fecal contamination is an important step toward understanding the impact that water, sanitation, and hygiene interventions have on reducing enteric infections. There is a need to standardize the methods used for surface sampling in field studies that examine fecal contamination in low-income settings. The dry cloth method presented in this manuscript improves upon the more commonly used swabbing technique that has been shown in the literature to have a low sampling efficiency. The recovery efficiency of a dry electrostatic cloth sampling method was evaluated using Escherichia coli and then applied to household surfaces in Iquitos, Peru, where there is high fecal contamination and enteric infection. Side-by-side measurements were taken from various floor locations within a household at the same time over a three-month period to compare for consistency of quantification of E. coli bacteria. The dry cloth sampling method in the laboratory setting showed 105% (95% Confidence Interval: 98%, 113%) E. coli recovery efficiency off of the cloths. The field application demonstrated strong agreement of side-by-side results (Pearson correlation coefficient for dirt surfaces was 0.83 ( p < 0.0001) and 0.91 ( p < 0.0001) for cement surfaces) and moderate agreement for results between entrance and kitchen samples (Pearson (0.53, p < 0.0001) and weighted Kappa statistic (0.54, p < 0.0001)). Our findings suggest that this method can be utilized in households with high bacterial loads using either continuous (quantitative) or categorical (semi-quantitative) data. The standardization of this low-cost, dry electrostatic cloth sampling method can be used to measure differences between households in intervention and non-intervention arms of randomized trials.

  3. Photoacoustic sample vessel and method of elevated pressure operation

    DOEpatents

    Autrey, Tom; Yonker, Clement R.

    2004-05-04

    An improved photoacoustic vessel and method of photoacoustic analysis. The photoacoustic sample vessel comprises an acoustic detector, an acoustic couplant, and an acoustic coupler having a chamber for holding the acoustic couplant and a sample. The acoustic couplant is selected from the group consisting of liquid, solid, and combinations thereof. Passing electromagnetic energy through the sample generates an acoustic signal within the sample, whereby the acoustic signal propagates through the sample to and through the acoustic couplant to the acoustic detector.

  4. Shear Strength of Remoulding Clay Samples Using Different Methods of Moulding

    NASA Astrophysics Data System (ADS)

    Norhaliza, W.; Ismail, B.; Azhar, A. T. S.; Nurul, N. J.

    2016-07-01

    Shear strength for clay soil was required to determine the soil stability. Clay was known as a soil with complex natural formations and very difficult to obtain undisturbed samples at the site. The aim of this paper was to determine the unconfined shear strength of remoulded clay on different methods in moulding samples which were proctor compaction, hand operated soil compacter and miniature mould methods. All the samples were remoulded with the same optimum moisture content (OMC) and density that were 18% and 1880 kg/m3 respectively. The unconfined shear strength results of remoulding clay soils for proctor compaction method was 289.56kPa with the strain 4.8%, hand operated method was 261.66kPa with the strain 4.4% and miniature mould method was 247.52kPa with the strain 3.9%. Based on the proctor compaction method, the reduction percentage of unconfined shear strength of remoulded clay soil of hand operated method was 9.66%, and for miniature mould method was 14.52%. Thus, because there was no significant difference of reduction percentage of unconfined shear strength between three different methods, so it can be concluded that remoulding clay by hand operated method and miniature mould method were accepted and suggested to perform remoulding clay samples by other future researcher. However for comparison, the hand operated method was more suitable to form remoulded clay sample in term of easiness, saving time and less energy for unconfined shear strength determination purposes.

  5. A new method to sample stuttering in preschool children.

    PubMed

    O'Brian, Sue; Jones, Mark; Pilowsky, Rachel; Onslow, Mark; Packman, Ann; Menzies, Ross

    2010-06-01

    This study reports a new method for sampling the speech of preschool stuttering children outside the clinic environment. Twenty parents engaged their stuttering children in an everyday play activity in the home with a telephone handset nearby. A remotely located researcher telephoned the parent and recorded the play session with a phone-recording jack attached to a digital audio recorder at the remote location. The parent placed an audio recorder near the child for comparison purposes. Children as young as 2 years complied with the remote method of speech sampling. The quality of the remote recordings was superior to that of the in-home recordings. There was no difference in means or reliability of stutter-count measures made from the remote recordings compared with those made in-home. Advantages of the new method include: (1) cost efficiency of real-time measurement of percent syllables stuttered in naturalistic situations, (2) reduction of bias associated with parent-selected timing of home recordings, (3) standardization of speech sampling procedures, (4) improved parent compliance with sampling procedures, (5) clinician or researcher on-line control of the acoustic and linguistic quality of recordings, and (6) elimination of the need to lend equipment to parents for speech sampling.

  6. Damage evolution analysis of coal samples under cyclic loading based on single-link cluster method

    NASA Astrophysics Data System (ADS)

    Zhang, Zhibo; Wang, Enyuan; Li, Nan; Li, Xuelong; Wang, Xiaoran; Li, Zhonghui

    2018-05-01

    In this paper, the acoustic emission (AE) response of coal samples under cyclic loading is measured. The results show that there is good positive relation between AE parameters and stress. The AE signal of coal samples under cyclic loading exhibits an obvious Kaiser Effect. The single-link cluster (SLC) method is applied to analyze the spatial evolution characteristics of AE events and the damage evolution process of coal samples. It is found that a subset scale of the SLC structure becomes smaller and smaller when the number of cyclic loading increases, and there is a negative linear relationship between the subset scale and the degree of damage. The spatial correlation length ξ of an SLC structure is calculated. The results show that ξ fluctuates around a certain value from the second cyclic loading process to the fifth cyclic loading process, but spatial correlation length ξ clearly increases in the sixth loading process. Based on the criterion of microcrack density, the coal sample failure process is the transformation from small-scale damage to large-scale damage, which is the reason for changes in the spatial correlation length. Through a systematic analysis, the SLC method is an effective method to research the damage evolution process of coal samples under cyclic loading, and will provide important reference values for studying coal bursts.

  7. Automated PCR setup for forensic casework samples using the Normalization Wizard and PCR Setup robotic methods.

    PubMed

    Greenspoon, S A; Sykes, K L V; Ban, J D; Pollard, A; Baisden, M; Farr, M; Graham, N; Collins, B L; Green, M M; Christenson, C C

    2006-12-20

    Human genome, pharmaceutical and research laboratories have long enjoyed the application of robotics to performing repetitive laboratory tasks. However, the utilization of robotics in forensic laboratories for processing casework samples is relatively new and poses particular challenges. Since the quantity and quality (a mixture versus a single source sample, the level of degradation, the presence of PCR inhibitors) of the DNA contained within a casework sample is unknown, particular attention must be paid to procedural susceptibility to contamination, as well as DNA yield, especially as it pertains to samples with little biological material. The Virginia Department of Forensic Science (VDFS) has successfully automated forensic casework DNA extraction utilizing the DNA IQ(trade mark) System in conjunction with the Biomek 2000 Automation Workstation. Human DNA quantitation is also performed in a near complete automated fashion utilizing the AluQuant Human DNA Quantitation System and the Biomek 2000 Automation Workstation. Recently, the PCR setup for casework samples has been automated, employing the Biomek 2000 Automation Workstation and Normalization Wizard, Genetic Identity version, which utilizes the quantitation data, imported into the software, to create a customized automated method for DNA dilution, unique to that plate of DNA samples. The PCR Setup software method, used in conjunction with the Normalization Wizard method and written for the Biomek 2000, functions to mix the diluted DNA samples, transfer the PCR master mix, and transfer the diluted DNA samples to PCR amplification tubes. Once the process is complete, the DNA extracts, still on the deck of the robot in PCR amplification strip tubes, are transferred to pre-labeled 1.5 mL tubes for long-term storage using an automated method. The automation of these steps in the process of forensic DNA casework analysis has been accomplished by performing extensive optimization, validation and testing of the

  8. Investigating Test Equating Methods in Small Samples through Various Factors

    ERIC Educational Resources Information Center

    Asiret, Semih; Sünbül, Seçil Ömür

    2016-01-01

    In this study, equating methods for random group design using small samples through factors such as sample size, difference in difficulty between forms, and guessing parameter was aimed for comparison. Moreover, which method gives better results under which conditions was also investigated. In this study, 5,000 dichotomous simulated data…

  9. Approaches of using the beard testing method to obtain complete length distributions of the original samples

    USDA-ARS?s Scientific Manuscript database

    The fiber testing instruments such as HVI can rapidly measure fiber length by testing a tapered fiber beard of the sample. But these instruments that use the beard testing method only report a limited number of fiber length parameters instead of the complete length distribution that is important fo...

  10. 40 CFR 80.8 - Sampling methods for gasoline and diesel fuel.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 17 2012-07-01 2012-07-01 false Sampling methods for gasoline and... gasoline and diesel fuel. The sampling methods specified in this section shall be used to collect samples of gasoline and diesel fuel for purposes of determining compliance with the requirements of this part...

  11. 40 CFR 80.8 - Sampling methods for gasoline and diesel fuel.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 16 2011-07-01 2011-07-01 false Sampling methods for gasoline and... gasoline and diesel fuel. The sampling methods specified in this section shall be used to collect samples of gasoline and diesel fuel for purposes of determining compliance with the requirements of this part...

  12. 40 CFR 80.8 - Sampling methods for gasoline and diesel fuel.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 17 2013-07-01 2013-07-01 false Sampling methods for gasoline and... gasoline and diesel fuel. The sampling methods specified in this section shall be used to collect samples of gasoline and diesel fuel for purposes of determining compliance with the requirements of this part...

  13. 76 FR 65165 - Importation of Plants for Planting; Risk-Based Sampling and Inspection Approach and Propagative...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-20

    ...] Importation of Plants for Planting; Risk-Based Sampling and Inspection Approach and Propagative Monitoring and... advising the public of our decision to implement a risk-based sampling approach for the inspection of... risk-based sampling and inspection approach will allow us to target high-risk plants for planting for...

  14. Comparability among four invertebrate sampling methods, Fountain Creek Basin, Colorado, 2010-2012

    USGS Publications Warehouse

    Zuellig, Robert E.; Bruce, James F.; Stogner, Sr., Robert W.; Brown, Krystal D.

    2014-01-01

    The U.S. Geological Survey, in cooperation with Colorado Springs City Engineering and Colorado Springs Utilities, designed a study to determine if sampling method and sample timing resulted in comparable samples and assessments of biological condition. To accomplish this task, annual invertebrate samples were collected concurrently using four sampling methods at 15 U.S. Geological Survey streamflow gages in the Fountain Creek basin from 2010 to 2012. Collectively, the four methods are used by local (U.S. Geological Survey cooperative monitoring program) and State monitoring programs (Colorado Department of Public Health and Environment) in the Fountain Creek basin to produce two distinct sample types for each program that target single-and multiple-habitats. This study found distinguishable differences between single-and multi-habitat sample types using both community similarities and multi-metric index values, while methods from each program within sample type were comparable. This indicates that the Colorado Department of Public Health and Environment methods were compatible with the cooperative monitoring program methods within multi-and single-habitat sample types. Comparisons between September and October samples found distinguishable differences based on community similarities for both sample types, whereas only differences were found for single-habitat samples when multi-metric index values were considered. At one site, differences between September and October index values from single-habitat samples resulted in opposing assessments of biological condition. Direct application of the results to inform the revision of the existing Fountain Creek basin U.S. Geological Survey cooperative monitoring program are discussed.

  15. Methods of sampling airborne fungi in working environments of waste treatment facilities.

    PubMed

    Černá, Kristýna; Wittlingerová, Zdeňka; Zimová, Magdaléna; Janovský, Zdeněk

    2016-01-01

    The objective of the present study was to evaluate and compare the efficiency of a filter based sampling method and a high volume sampling method for sampling airborne culturable fungi present in waste sorting facilities. Membrane filters method was compared with surface air system method. The selected sampling methods were modified and tested in 2 plastic waste sorting facilities. The total number of colony-forming units (CFU)/m3 of airborne fungi was dependent on the type of sampling device, on the time of sampling, which was carried out every hour from the beginning of the work shift, and on the type of cultivation medium (p < 0.001). Detected concentrations of airborne fungi ranged 2×102-1.7×106 CFU/m3 when using the membrane filters (MF) method, and 3×102-6.4×104 CFU/m3 when using the surface air system (SAS) method. Both methods showed comparable sensitivity to the fluctuations of the concentrations of airborne fungi during the work shifts. The SAS method is adequate for a fast indicative determination of concentration of airborne fungi. The MF method is suitable for thorough assessment of working environment contamination by airborne fungi. Therefore we recommend the MF method for the implementation of a uniform standard methodology of airborne fungi sampling in working environments of waste treatment facilities. This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.

  16. Surveying immigrants without sampling frames - evaluating the success of alternative field methods.

    PubMed

    Reichel, David; Morales, Laura

    2017-01-01

    This paper evaluates the sampling methods of an international survey, the Immigrant Citizens Survey, which aimed at surveying immigrants from outside the European Union (EU) in 15 cities in seven EU countries. In five countries, no sample frame was available for the target population. Consequently, alternative ways to obtain a representative sample had to be found. In three countries 'location sampling' was employed, while in two countries traditional methods were used with adaptations to reach the target population. The paper assesses the main methodological challenges of carrying out a survey among a group of immigrants for whom no sampling frame exists. The samples of the survey in these five countries are compared to results of official statistics in order to assess the accuracy of the samples obtained through the different sampling methods. It can be shown that alternative sampling methods can provide meaningful results in terms of core demographic characteristics although some estimates differ to some extent from the census results.

  17. Flow cytometric detection method for DNA samples

    DOEpatents

    Nasarabadi, Shanavaz [Livermore, CA; Langlois, Richard G [Livermore, CA; Venkateswaran, Kodumudi S [Round Rock, TX

    2011-07-05

    Disclosed herein are two methods for rapid multiplex analysis to determine the presence and identity of target DNA sequences within a DNA sample. Both methods use reporting DNA sequences, e.g., modified conventional Taqman.RTM. probes, to combine multiplex PCR amplification with microsphere-based hybridization using flow cytometry means of detection. Real-time PCR detection can also be incorporated. The first method uses a cyanine dye, such as, Cy3.TM., as the reporter linked to the 5' end of a reporting DNA sequence. The second method positions a reporter dye, e.g., FAM.TM. on the 3' end of the reporting DNA sequence and a quencher dye, e.g., TAMRA.TM., on the 5' end.

  18. Flow cytometric detection method for DNA samples

    DOEpatents

    Nasarabadi, Shanavaz [Livermore, CA; Langlois, Richard G [Livermore, CA; Venkateswaran, Kodumudi S [Livermore, CA

    2006-08-01

    Disclosed herein are two methods for rapid multiplex analysis to determine the presence and identity of target DNA sequences within a DNA sample. Both methods use reporting DNA sequences, e.g., modified conventional Taqman.RTM. probes, to combine multiplex PCR amplification with microsphere-based hybridization using flow cytometry means of detection. Real-time PCR detection can also be incorporated. The first method uses a cyanine dye, such as, Cy3.TM., as the reporter linked to the 5' end of a reporting DNA sequence. The second method positions a reporter dye, e.g., FAM, on the 3' end of the reporting DNA sequence and a quencher dye, e.g., TAMRA, on the 5' end.

  19. Nano-objects as biomaterials: immense opportunities, significant challenges and the important use of surface analytical methods

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Baer, Donald R.; Shutthanandan, Vaithiyalingam

    Nano-sized objects are increasingly important as biomaterials and their surfaces play critical roles in determining their beneficial or deleterious behaviors in biological systems. Important characteristics of nanomaterials that impact their application in many areas are described with a strong focus on the importance of particle surfaces and surface characterization. Understanding aspects of the inherent nature of nano-objects and the important role that surfaces play in these applications is a universal need for any research or product development using such materials in biological applications. The role of surface analysis methods in collecting critical information about the nature of particle surfaces andmore » physicochemical properties of nano-objects is described along with the importance of including sample history and analysis results in a record of provenance information regarding specific batches of nano-objects.« less

  20. Monitoring benthic aIgal communides: A comparison of targeted and coefficient sampling methods

    USGS Publications Warehouse

    Edwards, Matthew S.; Tinker, M. Tim

    2009-01-01

    Choosing an appropriate sample unit is a fundamental decision in the design of ecological studies. While numerous methods have been developed to estimate organism abundance, they differ in cost, accuracy and precision.Using both field data and computer simulation modeling, we evaluated the costs and benefits associated with two methods commonly used to sample benthic organisms in temperate kelp forests. One of these methods, the Targeted Sampling method, relies on different sample units, each "targeted" for a specific species or group of species while the other method relies on coefficients that represent ranges of bottom cover obtained from visual esti-mates within standardized sample units. Both the field data and the computer simulations suggest that both methods yield remarkably similar estimates of organism abundance and among-site variability, although the Coefficient method slightly underestimates variability among sample units when abundances are low. In contrast, the two methods differ considerably in the effort needed to sample these communities; the Targeted Sampling requires more time and twice the personnel to complete. We conclude that the Coefficent Sampling method may be better for environmental monitoring programs where changes in mean abundance are of central concern and resources are limiting, but that the Targeted sampling methods may be better for ecological studies where quantitative relationships among species and small-scale variability in abundance are of central concern.

  1. Efficient free energy calculations by combining two complementary tempering sampling methods

    NASA Astrophysics Data System (ADS)

    Xie, Liangxu; Shen, Lin; Chen, Zhe-Ning; Yang, Mingjun

    2017-01-01

    Although energy barriers can be efficiently crossed in the reaction coordinate (RC) guided sampling, this type of method suffers from identification of the correct RCs or requirements of high dimensionality of the defined RCs for a given system. If only the approximate RCs with significant barriers are used in the simulations, hidden energy barriers with small to medium height would exist in other degrees of freedom (DOFs) relevant to the target process and consequently cause the problem of insufficient sampling. To address the sampling in this so-called hidden barrier situation, here we propose an effective approach to combine temperature accelerated molecular dynamics (TAMD), an efficient RC-guided sampling method, with the integrated tempering sampling (ITS), a generalized ensemble sampling method. In this combined ITS-TAMD method, the sampling along the major RCs with high energy barriers is guided by TAMD and the sampling of the rest of the DOFs with lower but not negligible barriers is enhanced by ITS. The performance of ITS-TAMD to three systems in the processes with hidden barriers has been examined. In comparison to the standalone TAMD or ITS approach, the present hybrid method shows three main improvements. (1) Sampling efficiency can be improved at least five times even if in the presence of hidden energy barriers. (2) The canonical distribution can be more accurately recovered, from which the thermodynamic properties along other collective variables can be computed correctly. (3) The robustness of the selection of major RCs suggests that the dimensionality of necessary RCs can be reduced. Our work shows more potential applications of the ITS-TAMD method as the efficient and powerful tool for the investigation of a broad range of interesting cases.

  2. Efficient free energy calculations by combining two complementary tempering sampling methods.

    PubMed

    Xie, Liangxu; Shen, Lin; Chen, Zhe-Ning; Yang, Mingjun

    2017-01-14

    Although energy barriers can be efficiently crossed in the reaction coordinate (RC) guided sampling, this type of method suffers from identification of the correct RCs or requirements of high dimensionality of the defined RCs for a given system. If only the approximate RCs with significant barriers are used in the simulations, hidden energy barriers with small to medium height would exist in other degrees of freedom (DOFs) relevant to the target process and consequently cause the problem of insufficient sampling. To address the sampling in this so-called hidden barrier situation, here we propose an effective approach to combine temperature accelerated molecular dynamics (TAMD), an efficient RC-guided sampling method, with the integrated tempering sampling (ITS), a generalized ensemble sampling method. In this combined ITS-TAMD method, the sampling along the major RCs with high energy barriers is guided by TAMD and the sampling of the rest of the DOFs with lower but not negligible barriers is enhanced by ITS. The performance of ITS-TAMD to three systems in the processes with hidden barriers has been examined. In comparison to the standalone TAMD or ITS approach, the present hybrid method shows three main improvements. (1) Sampling efficiency can be improved at least five times even if in the presence of hidden energy barriers. (2) The canonical distribution can be more accurately recovered, from which the thermodynamic properties along other collective variables can be computed correctly. (3) The robustness of the selection of major RCs suggests that the dimensionality of necessary RCs can be reduced. Our work shows more potential applications of the ITS-TAMD method as the efficient and powerful tool for the investigation of a broad range of interesting cases.

  3. SnagPRO: snag and tree sampling and analysis methods for wildlife

    Treesearch

    Lisa J. Bate; Michael J. Wisdom; Edward O. Garton; Shawn C. Clabough

    2008-01-01

    We describe sampling methods and provide software to accurately and efficiently estimate snag and tree densities at desired scales to meet a variety of research and management objectives. The methods optimize sampling effort by choosing a plot size appropriate for the specified forest conditions and sampling goals. Plot selection and data analyses are supported by...

  4. Soil separator and sampler and method of sampling

    DOEpatents

    O'Brien, Barry H [Idaho Falls, ID; Ritter, Paul D [Idaho Falls, ID

    2010-02-16

    A soil sampler includes a fluidized bed for receiving a soil sample. The fluidized bed may be in communication with a vacuum for drawing air through the fluidized bed and suspending particulate matter of the soil sample in the air. In a method of sampling, the air may be drawn across a filter, separating the particulate matter. Optionally, a baffle or a cyclone may be included within the fluidized bed for disentrainment, or dedusting, so only the finest particulate matter, including asbestos, will be trapped on the filter. The filter may be removable, and may be tested to determine the content of asbestos and other hazardous particulate matter in the soil sample.

  5. Molecular cancer classification using a meta-sample-based regularized robust coding method.

    PubMed

    Wang, Shu-Lin; Sun, Liuchao; Fang, Jianwen

    2014-01-01

    Previous studies have demonstrated that machine learning based molecular cancer classification using gene expression profiling (GEP) data is promising for the clinic diagnosis and treatment of cancer. Novel classification methods with high efficiency and prediction accuracy are still needed to deal with high dimensionality and small sample size of typical GEP data. Recently the sparse representation (SR) method has been successfully applied to the cancer classification. Nevertheless, its efficiency needs to be improved when analyzing large-scale GEP data. In this paper we present the meta-sample-based regularized robust coding classification (MRRCC), a novel effective cancer classification technique that combines the idea of meta-sample-based cluster method with regularized robust coding (RRC) method. It assumes that the coding residual and the coding coefficient are respectively independent and identically distributed. Similar to meta-sample-based SR classification (MSRC), MRRCC extracts a set of meta-samples from the training samples, and then encodes a testing sample as the sparse linear combination of these meta-samples. The representation fidelity is measured by the l2-norm or l1-norm of the coding residual. Extensive experiments on publicly available GEP datasets demonstrate that the proposed method is more efficient while its prediction accuracy is equivalent to existing MSRC-based methods and better than other state-of-the-art dimension reduction based methods.

  6. NEW COLUMN SEPARATION METHOD FOR EMERGENCY URINE SAMPLES

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Maxwell, S; Brian Culligan, B

    2007-08-28

    The Savannah River Site Environmental Bioassay Lab participated in the 2007 NRIP Emergency Response program administered by the National Institute for Standards and Technology (NIST) in May, 2007. A new rapid column separation method was applied directly to the NRIP 2007 emergency urine samples, with only minimal sample preparation to reduce preparation time. Calcium phosphate precipitation, previously used to pre-concentrate actinides and Sr-90 in NRIP 2006 urine and water samples, was not used for the NRIP 2007 urine samples. Instead, the raw urine was acidified and passed directly through the stacked resin columns (TEVA+TRU+SR Resins) to separate the actinides andmore » strontium from the NRIP urine samples more quickly. This improvement reduced sample preparation time for the NRIP 2007 emergency urine analyses significantly. This approach works well for small volume urine samples expected during an emergency response event. Based on initial feedback from NIST, the SRS Environmental Bioassay Lab had the most rapid analysis times for actinides and strontium-90 analyses for NRIP 2007 urine samples.« less

  7. Whither RDS? An investigation of Respondent Driven Sampling as a method of recruiting mainstream marijuana users

    PubMed Central

    2010-01-01

    Background An important challenge in conducting social research of specific relevance to harm reduction programs is locating hidden populations of consumers of substances like cannabis who typically report few adverse or unwanted consequences of their use. Much of the deviant, pathologized perception of drug users is historically derived from, and empirically supported, by a research emphasis on gaining ready access to users in drug treatment or in prison populations with higher incidence of problems of dependence and misuse. Because they are less visible, responsible recreational users of illicit drugs have been more difficult to study. Methods This article investigates Respondent Driven Sampling (RDS) as a method of recruiting experienced marijuana users representative of users in the general population. Based on sampling conducted in a multi-city study (Halifax, Montreal, Toronto, and Vancouver), and compared to samples gathered using other research methods, we assess the strengths and weaknesses of RDS recruitment as a means of gaining access to illicit substance users who experience few harmful consequences of their use. Demographic characteristics of the sample in Toronto are compared with those of users in a recent household survey and a pilot study of Toronto where the latter utilized nonrandom self-selection of respondents. Results A modified approach to RDS was necessary to attain the target sample size in all four cities (i.e., 40 'users' from each site). The final sample in Toronto was largely similar, however, to marijuana users in a random household survey that was carried out in the same city. Whereas well-educated, married, whites and females in the survey were all somewhat overrepresented, the two samples, overall, were more alike than different with respect to economic status and employment. Furthermore, comparison with a self-selected sample suggests that (even modified) RDS recruitment is a cost-effective way of gathering respondents who are

  8. A comparison of sample preparation methods for extracting volatile organic compounds (VOCs) from equine faeces using HS-SPME.

    PubMed

    Hough, Rachael; Archer, Debra; Probert, Christopher

    2018-01-01

    Disturbance to the hindgut microbiota can be detrimental to equine health. Metabolomics provides a robust approach to studying the functional aspect of hindgut microorganisms. Sample preparation is an important step towards achieving optimal results in the later stages of analysis. The preparation of samples is unique depending on the technique employed and the sample matrix to be analysed. Gas chromatography mass spectrometry (GCMS) is one of the most widely used platforms for the study of metabolomics and until now an optimised method has not been developed for equine faeces. To compare a sample preparation method for extracting volatile organic compounds (VOCs) from equine faeces. Volatile organic compounds were determined by headspace solid phase microextraction gas chromatography mass spectrometry (HS-SPME-GCMS). Factors investigated were the mass of equine faeces, type of SPME fibre coating, vial volume and storage conditions. The resultant method was unique to those developed for other species. Aliquots of 1000 or 2000 mg in 10 ml or 20 ml SPME headspace were optimal. From those tested, the extraction of VOCs should ideally be performed using a divinylbenzene-carboxen-polydimethysiloxane (DVB-CAR-PDMS) SPME fibre. Storage of faeces for up to 12 months at - 80 °C shared a greater percentage of VOCs with a fresh sample than the equivalent stored at - 20 °C. An optimised method for extracting VOCs from equine faeces using HS-SPME-GCMS has been developed and will act as a standard to enable comparisons between studies. This work has also highlighted storage conditions as an important factor to consider in experimental design for faecal metabolomics studies.

  9. Passive Samplers for Investigations of Air Quality: Method Description, Implementation, and Comparison to Alternative Sampling Methods

    EPA Science Inventory

    This Paper covers the basics of passive sampler design, compares passive samplers to conventional methods of air sampling, and discusses considerations when implementing a passive sampling program. The Paper also discusses field sampling and sample analysis considerations to ensu...

  10. Post-sampling release of free fatty acids - effects of heat stabilization and methods of euthanasia.

    PubMed

    Jernerén, Fredrik; Söderquist, Marcus; Karlsson, Oskar

    2015-01-01

    The field of lipid research has made progress and it is now possible to study the lipidome of cells and organelles. A basic requirement of a successful lipid study is adequate pre-analytical sample handling, as some lipids can be unstable and postmortem changes can cause substantial accumulation of free fatty acids (FFAs). The aim of the present study was to investigate the effects of conductive heat stabilization and euthanasia methods on FFA levels in the rat brain and liver using liquid chromatography tandem mass spectrometry. The analysis of brain homogenates clearly demonstrated phospholipase activity and time-dependent post-sampling changes in the lipid pool of snap frozen non-stabilized tissue. There was a significant increase in FFAs already at 2min, which continued over time. Heat stabilization was shown to be an efficient method to reduce phospholipase activity and ex vivo lipolysis. Post-sampling effects due to tissue thawing and sample preparation induced a massive release of FFAs (up to 3700%) from non-stabilized liver and brain tissues compared to heat stabilized tissue. Furthermore, the choice of euthanasia method significantly influenced the levels of FFAs in the brain. The FFAs were decreased by 15-44% in the group of animals euthanized by pentobarbital injection compared with CO2 inhalation or decapitation. Our results highlight the importance of considering euthanasia methods and pre-analytical treatment in lipid analysis, factors which may otherwise interfere with the outcome of the experiments. Copyright © 2014 Elsevier Inc. All rights reserved.

  11. Toxicological importance of human biomonitoring of metallic and metalloid elements in different biological samples.

    PubMed

    Gil, F; Hernández, A F

    2015-06-01

    Human biomonitoring has become an important tool for the assessment of internal doses of metallic and metalloid elements. These elements are of great significance because of their toxic properties and wide distribution in environmental compartments. Although blood and urine are the most used and accepted matrices for human biomonitoring, other non-conventional samples (saliva, placenta, meconium, hair, nails, teeth, breast milk) may have practical advantages and would provide additional information on health risk. Nevertheless, the analysis of these compounds in biological matrices other than blood and urine has not yet been accepted as a useful tool for biomonitoring. The validation of analytical procedures is absolutely necessary for a proper implementation of non-conventional samples in biomonitoring programs. However, the lack of reliable and useful analytical methodologies to assess exposure to metallic elements, and the potential interference of external contamination and variation in biological features of non-conventional samples are important limitations for setting health-based reference values. The influence of potential confounding factors on metallic concentration should always be considered. More research is needed to ascertain whether or not non-conventional matrices offer definitive advantages over the traditional samples and to broaden the available database for establishing worldwide accepted reference values in non-exposed populations. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Acute Pain Perception During Different Sampling Methods for Respiratory Culture in Cystic Fibrosis Patients.

    PubMed

    Eyns, Hanneke; De Wachter, Elke; Malfroot, Anne; Vaes, Peter

    2018-03-01

     = -0.226 [P = 0.097] and ρ = -0.135 [P = 0.798], respectively). A relatively large range of pain experiences was observed in patients with CF during respiratory culture sampling, which underlines the importance of individual pain assessment. Nevertheless, clinicians can confidently choose the sampling method based on validity over patients' preference. Copyright © 2017 American Academy of Hospice and Palliative Medicine. Published by Elsevier Inc. All rights reserved.

  13. Analysis of polyethylene microplastics in environmental samples, using a thermal decomposition method.

    PubMed

    Dümichen, Erik; Barthel, Anne-Kathrin; Braun, Ulrike; Bannick, Claus G; Brand, Kathrin; Jekel, Martin; Senz, Rainer

    2015-11-15

    Small polymer particles with a diameter of less than 5 mm called microplastics find their way into the environment from polymer debris and industrial production. Therefore a method is needed to identify and quantify microplastics in various environmental samples to generate reliable concentration values. Such concentration values, i.e. quantitative results, are necessary for an assessment of microplastic in environmental media. This was achieved by thermal extraction in thermogravimetric analysis (TGA), connected to a solid-phase adsorber. These adsorbers were subsequently analysed by thermal desorption gas chromatography mass spectrometry (TDS-GC-MS). In comparison to other chromatographic methods, like pyrolyse gas chromatography mass spectrometry (Py-GC-MS), the relatively high sample masses in TGA (about 200 times higher than used in Py-GC-MS) analysed here enable the measurement of complex matrices that are not homogenous on a small scale. Through the characteristic decomposition products known for every kind of polymer it is possible to identify and even to quantify polymer particles in various matrices. Polyethylene (PE), one of the most important representatives for microplastics, was chosen as an example for identification and quantification. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Detection of protozoa in water samples by formalin/ether concentration method.

    PubMed

    Lora-Suarez, Fabiana; Rivera, Raul; Triviño-Valencia, Jessica; Gomez-Marin, Jorge E

    2016-09-01

    Methods to detect protozoa in water samples are expensive and laborious. We evaluated the formalin/ether concentration method to detect Giardia sp., Cryptosporidium sp. and Toxoplasma in water. In order to test the properties of the method, we spiked water samples with different amounts of each protozoa (0, 10 and 50 cysts or oocysts) in a volume of 10 L of water. Immunofluorescence assay was used for detection of Giardia and Cryptosporidium. Toxoplasma oocysts were identified by morphology. The mean percent of recovery in 10 repetitions of the entire method, in 10 samples spiked with ten parasites and read by three different observers, were for Cryptosporidium 71.3 ± 12, for Giardia 63 ± 10 and for Toxoplasma 91.6 ± 9 and the relative standard deviation of the method was of 17.5, 17.2 and 9.8, respectively. Intraobserver variation as measured by intraclass correlation coefficient, was fair for Toxoplasma, moderate for Cryptosporidium and almost perfect for Giardia. The method was then applied in 77 samples of raw and drinkable water in three different plant of water treatment. Cryptosporidium was found in 28 of 77 samples (36%) and Giardia in 31 of 77 samples (40%). Theses results identified significant differences in treatment process to reduce the presence of Giardia and Cryptosporidium. In conclusion, the formalin ether method to concentrate protozoa in water is a new alternative for low resources countries, where is urgently need to monitor and follow the presence of theses protozoa in drinkable water. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Oral sampling methods are associated with differences in immune marker concentrations.

    PubMed

    Fakhry, Carole; Qeadan, Fares; Gilman, Robert H; Yori, Pablo; Kosek, Margaret; Patterson, Nicole; Eisele, David W; Gourin, Christine G; Chitguppi, Chandala; Marks, Morgan; Gravitt, Patti

    2018-06-01

    To determine whether the concentration and distribution of immune markers in paired oral samples were similar. Clinical research. Cross-sectional study. Paired saliva and oral secretions (OS) samples were collected. The concentration of immune markers was estimated using Luminex multiplex assay (Thermo Fisher Scientific, Waltham, MA). For each sample, the concentration of respective immune markers was normalized to total protein present and log-transformed. Median concentrations of immune markers were compared between both types of samples. Intermarker correlation in each sampling method and across sampling methods was evaluated. There were 90 study participants. Concentrations of immune markers in saliva samples were significantly different from concentrations in OS samples. Oral secretions samples showed higher concentrations of immunoregulatory markers, whereas the saliva samples contained proinflammatory markers in higher concentration. The immune marker profile in saliva samples is distinct from the immune marker profile in paired OS samples. 2b. Laryngoscope, 128:E214-E221, 2018. © 2017 The American Laryngological, Rhinological and Otological Society, Inc.

  16. Comparison of sampling methods for radiocarbon dating of carbonyls in air samples via accelerator mass spectrometry

    NASA Astrophysics Data System (ADS)

    Schindler, Matthias; Kretschmer, Wolfgang; Scharf, Andreas; Tschekalinskij, Alexander

    2016-05-01

    Three new methods to sample and prepare various carbonyl compounds for radiocarbon measurements were developed and tested. Two of these procedures utilized the Strecker synthetic method to form amino acids from carbonyl compounds with either sodium cyanide or trimethylsilyl cyanide. The third procedure used semicarbazide to form crystalline carbazones with the carbonyl compounds. The resulting amino acids and semicarbazones were then separated and purified using thin layer chromatography. The separated compounds were then combusted to CO2 and reduced to graphite to determine 14C content by accelerator mass spectrometry (AMS). All of these methods were also compared with the standard carbonyl compound sampling method wherein a compound is derivatized with 2,4-dinitrophenylhydrazine and then separated by high-performance liquid chromatography (HPLC).

  17. Experimental Investigations on Subsequent Yield Surface of Pure Copper by Single-Sample and Multi-Sample Methods under Various Pre-Deformation.

    PubMed

    Liu, Gui-Long; Huang, Shi-Hong; Shi, Che-Si; Zeng, Bin; Zhang, Ke-Shi; Zhong, Xian-Ci

    2018-02-10

    Using copper thin-walled tubular specimens, the subsequent yield surfaces under pre-tension, pre-torsion and pre-combined tension-torsion are measured, where the single-sample and multi-sample methods are applied respectively to determine the yield stresses at specified offset strain. The rule and characteristics of the evolution of the subsequent yield surface are investigated. Under the conditions of different pre-strains, the influence of test point number, test sequence and specified offset strain on the measurement of subsequent yield surface and the concave phenomenon for measured yield surface are studied. Moreover, the feasibility and validity of the two methods are compared. The main conclusions are drawn as follows: (1) For the single or multi-sample method, the measured subsequent yield surfaces are remarkably different from cylindrical yield surfaces proposed by the classical plasticity theory; (2) there are apparent differences between the test results from the two kinds of methods: the multi-sample method is not influenced by the number of test points, test order and the cumulative effect of residual plastic strain resulting from the other test point, while those are very influential in the single-sample method; and (3) the measured subsequent yield surface may appear concave, which can be transformed to convex for single-sample method by changing the test sequence. However, for the multiple-sample method, the concave phenomenon will disappear when a larger offset strain is specified.

  18. A Novel Videography Method for Generating Crack-Extension Resistance Curves in Small Bone Samples

    PubMed Central

    Katsamenis, Orestis L.; Jenkins, Thomas; Quinci, Federico; Michopoulou, Sofia; Sinclair, Ian; Thurner, Philipp J.

    2013-01-01

    Assessment of bone quality is an emerging solution for quantifying the effects of bone pathology or treatment. Perhaps one of the most important parameters characterising bone quality is the toughness behaviour of bone. Particularly, fracture toughness, is becoming a popular means for evaluating bone quality. The method is moving from a single value approach that models bone as a linear-elastic material (using the stress intensity factor, K) towards full crack extension resistance curves (R-curves) using a non-linear model (the strain energy release rate in J-R curves). However, for explanted human bone or small animal bones, there are difficulties in measuring crack-extension resistance curves due to size constraints at the millimetre and sub-millimetre scale. This research proposes a novel “whitening front tracking” method that uses videography to generate full fracture resistance curves in small bone samples where crack propagation cannot typically be observed. Here we present this method on sharp edge notched samples (<1 mm×1 mm×Length) prepared from four human femora tested in three-point bending. Each sample was loaded in a mechanical tester with the crack propagation recorded using videography and analysed using an algorithm to track the whitening (damage) zone. Using the “whitening front tracking” method, full R-curves and J-R curves could be generated for these samples. The curves for this antiplane longitudinal orientation were similar to those found in the literature, being between the published longitudinal and transverse orientations. The proposed technique shows the ability to generate full “crack” extension resistance curves by tracking the whitening front propagation to overcome the small size limitations and the single value approach. PMID:23405186

  19. Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems.

    PubMed

    Mori, Takaharu; Jung, Jaewoon; Sugita, Yuji

    2013-12-10

    Conformational sampling is fundamentally important for simulating complex biomolecular systems. The generalized-ensemble algorithm, especially the temperature replica-exchange molecular dynamics method (T-REMD), is one of the most powerful methods to explore structures of biomolecules such as proteins, nucleic acids, carbohydrates, and also of lipid membranes. T-REMD simulations have focused on soluble proteins rather than membrane proteins or lipid bilayers, because explicit membranes do not keep their structural integrity at high temperature. Here, we propose a new generalized-ensemble algorithm for membrane systems, which we call the surface-tension REMD method. Each replica is simulated in the NPγT ensemble, and surface tensions in a pair of replicas are exchanged at certain intervals to enhance conformational sampling of the target membrane system. We test the method on two biological membrane systems: a fully hydrated DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine) lipid bilayer and a WALP23-POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membrane system. During these simulations, a random walk in surface tension space is realized. Large-scale lateral deformation (shrinking and stretching) of the membranes takes place in all of the replicas without collapse of the lipid bilayer structure. There is accelerated lateral diffusion of DPPC lipid molecules compared with conventional MD simulation, and a much wider range of tilt angle of the WALP23 peptide is sampled due to large deformation of the POPC lipid bilayer and through peptide-lipid interactions. Our method could be applicable to a wide variety of biological membrane systems.

  20. Method and sample spinning apparatus for measuring the NMR spectrum of an orientationally disordered sample

    DOEpatents

    Pines, Alexander; Samoson, Ago

    1990-01-01

    An improved NMR apparatus and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise orientationally disordered samples. The apparatus spins the sample about an axis. The angle of the axis is mechanically varied such that the time average of two or more Legendre polynomials are zero.

  1. New Methods of Sample Preparation for Atom Probe Specimens

    NASA Technical Reports Server (NTRS)

    Kuhlman, Kimberly, R.; Kowalczyk, Robert S.; Ward, Jennifer R.; Wishard, James L.; Martens, Richard L.; Kelly, Thomas F.

    2003-01-01

    Magnetite is a common conductive mineral found on Earth and Mars. Disk-shaped precipitates approximately 40 nm in diameter have been shown to have manganese and aluminum concentrations. Atom-probe field-ion microscopy (APFIM) is the only technique that can potentially quantify the composition of these precipitates. APFIM will be used to characterize geological and planetary materials, analyze samples of interest for geomicrobiology; and, for the metrology of nanoscale instrumentation. Prior to APFIM sample preparation was conducted by electropolishing, the method of sharp shards (MSS), or Bosch process (deep reactive ion etching) with focused ion beam (FIB) milling as a final step. However, new methods are required for difficult samples. Many materials are not easily fabricated using electropolishing, MSS, or the Bosch process, FIB milling is slow and expensive, and wet chemistry and the reactive ion etching are typically limited to Si and other semiconductors. APFIM sample preparation using the dicing saw is commonly used to section semiconductor wafers into individual devices following manufacture. The dicing saw is a time-effective method for preparing high aspect ratio posts of poorly conducting materials. Femtosecond laser micromachining is also suitable for preparation of posts. FIB time required is reduced by about a factor of 10 and multi-tip specimens can easily be fabricated using the dicing saw.

  2. Evaluation of sample preparation methods for the analysis of papaya leaf proteins through two-dimensional gel electrophoresis.

    PubMed

    Rodrigues, Silas Pessini; Ventura, José Aires; Zingali, R B; Fernandes, P M B

    2009-01-01

    A variety of sample preparation protocols for plant proteomic analysis using two-dimensional gel electrophoresis (2-DE) have been reported. However, they usually have to be adapted and further optimised for the analysis of plant species not previously studied. This work aimed to evaluate different sample preparation protocols for analysing Carica papaya L. leaf proteins through 2-DE. Four sample preparation methods were tested: (1) phenol extraction and methanol-ammonium acetate precipitation; (2) no precipitation fractionation; and the traditional trichloroacetic acid-acetone precipitation either (3) with or (4) without protein fractionation. The samples were analysed for their compatibility with SDS-PAGE (1-DE) and 2-DE. Fifteen selected protein spots were trypsinised and analysed by matrix-assisted laser desorption/ionisation time-of-flight tandem mass spectrometry (MALDI-TOF-MS/MS), followed by a protein search using the NCBInr database to accurately identify all proteins. Methods number 3 and 4 resulted in large quantities of protein with good 1-DE separation and were chosen for 2-DE analysis. However, only the TCA method without fractionation (no. 4) proved to be useful. Spot number and resolution advances were achieved, which included having an additional solubilisation step in the conventional TCA method. Moreover, most of the theoretical and experimental protein molecular weight and pI data had similar values, suggesting good focusing and, most importantly, limited protein degradation. The described sample preparation method allows the proteomic analysis of papaya leaves by 2-DE and mass spectrometry (MALDI-TOF-MS/MS). The methods presented can be a starting point for the optimisation of sample preparation protocols for other plant species.

  3. Compendium of selected methods for sampling and analysis at geothermal facilities

    NASA Astrophysics Data System (ADS)

    Kindle, C. H.; Pool, K. H.; Ludwick, J. D.; Robertson, D. E.

    1984-06-01

    An independent study of the field has resulted in a compilation of the best methods for sampling, preservation and analysis of potential pollutants from geothermally fueled electric power plants. These methods are selected as the most usable over the range of application commonly experienced in the various geothermal plant sample locations. In addition to plant and well piping, techniques for sampling cooling towers, ambient gases, solids, surface and subsurface waters are described. Emphasis is placed on the use of sampling proves to extract samples from heterogeneous flows. Certain sampling points, constituents and phases of plant operation are more amenable to quality assurance improvement in the emission measurements than others and are so identified.

  4. A Mixed Methods Investigation of Mixed Methods Sampling Designs in Social and Health Science Research

    ERIC Educational Resources Information Center

    Collins, Kathleen M. T.; Onwuegbuzie, Anthony J.; Jiao, Qun G.

    2007-01-01

    A sequential design utilizing identical samples was used to classify mixed methods studies via a two-dimensional model, wherein sampling designs were grouped according to the time orientation of each study's components and the relationship of the qualitative and quantitative samples. A quantitative analysis of 121 studies representing nine fields…

  5. Transformation-cost time-series method for analyzing irregularly sampled data

    NASA Astrophysics Data System (ADS)

    Ozken, Ibrahim; Eroglu, Deniz; Stemler, Thomas; Marwan, Norbert; Bagci, G. Baris; Kurths, Jürgen

    2015-06-01

    Irregular sampling of data sets is one of the challenges often encountered in time-series analysis, since traditional methods cannot be applied and the frequently used interpolation approach can corrupt the data and bias the subsequence analysis. Here we present the TrAnsformation-Cost Time-Series (TACTS) method, which allows us to analyze irregularly sampled data sets without degenerating the quality of the data set. Instead of using interpolation we consider time-series segments and determine how close they are to each other by determining the cost needed to transform one segment into the following one. Using a limited set of operations—with associated costs—to transform the time series segments, we determine a new time series, that is our transformation-cost time series. This cost time series is regularly sampled and can be analyzed using standard methods. While our main interest is the analysis of paleoclimate data, we develop our method using numerical examples like the logistic map and the Rössler oscillator. The numerical data allows us to test the stability of our method against noise and for different irregular samplings. In addition we provide guidance on how to choose the associated costs based on the time series at hand. The usefulness of the TACTS method is demonstrated using speleothem data from the Secret Cave in Borneo that is a good proxy for paleoclimatic variability in the monsoon activity around the maritime continent.

  6. Transformation-cost time-series method for analyzing irregularly sampled data.

    PubMed

    Ozken, Ibrahim; Eroglu, Deniz; Stemler, Thomas; Marwan, Norbert; Bagci, G Baris; Kurths, Jürgen

    2015-06-01

    Irregular sampling of data sets is one of the challenges often encountered in time-series analysis, since traditional methods cannot be applied and the frequently used interpolation approach can corrupt the data and bias the subsequence analysis. Here we present the TrAnsformation-Cost Time-Series (TACTS) method, which allows us to analyze irregularly sampled data sets without degenerating the quality of the data set. Instead of using interpolation we consider time-series segments and determine how close they are to each other by determining the cost needed to transform one segment into the following one. Using a limited set of operations-with associated costs-to transform the time series segments, we determine a new time series, that is our transformation-cost time series. This cost time series is regularly sampled and can be analyzed using standard methods. While our main interest is the analysis of paleoclimate data, we develop our method using numerical examples like the logistic map and the Rössler oscillator. The numerical data allows us to test the stability of our method against noise and for different irregular samplings. In addition we provide guidance on how to choose the associated costs based on the time series at hand. The usefulness of the TACTS method is demonstrated using speleothem data from the Secret Cave in Borneo that is a good proxy for paleoclimatic variability in the monsoon activity around the maritime continent.

  7. Self-contained cryogenic gas sampling apparatus and method

    DOEpatents

    McManus, G.J.; Motes, B.G.; Bird, S.K.; Kotter, D.K.

    1996-03-26

    Apparatus for obtaining a whole gas sample, is composed of: a sample vessel having an inlet for receiving a gas sample; a controllable valve mounted for controllably opening and closing the inlet; a valve control coupled to the valve for opening and closing the valve at selected times; a portable power source connected for supplying operating power to the valve control; and a cryogenic coolant in thermal communication with the vessel for cooling the interior of the vessel to cryogenic temperatures. A method is described for obtaining an air sample using the apparatus described above, by: placing the apparatus at a location at which the sample is to be obtained; operating the valve control to open the valve at a selected time and close the valve at a selected subsequent time; and between the selected times maintaining the vessel at a cryogenic temperature by heat exchange with the coolant. 3 figs.

  8. Self-contained cryogenic gas sampling apparatus and method

    DOEpatents

    McManus, Gary J.; Motes, Billy G.; Bird, Susan K.; Kotter, Dale K.

    1996-01-01

    Apparatus for obtaining a whole gas sample, composed of: a sample vessel having an inlet for receiving a gas sample; a controllable valve mounted for controllably opening and closing the inlet; a valve control coupled to the valve for opening and closing the valve at selected times; a portable power source connected for supplying operating power to the valve control; and a cryogenic coolant in thermal communication with the vessel for cooling the interior of the vessel to cryogenic temperatures. A method of obtaining an air sample using the apparatus described above, by: placing the apparatus at a location at which the sample is to be obtained; operating the valve control to open the valve at a selected time and close the valve at a selected subsequent time; and between the selected times maintaining the vessel at a cryogenic temperature by heat exchange with the coolant.

  9. A remark on the theory of measuring thermal diffusivity by the modified Angstrom's method. [in lunar samples

    NASA Technical Reports Server (NTRS)

    Horai, K.-I.

    1981-01-01

    A theory of the measurement of the thermal diffusivity of a sample by the modified Angstrom method is developed for the case in which radiative heat loss from the end surface of the sample is not negligible, and applied to measurements performed on lunar samples. Formulas allowing sample thermal diffusivity to be determined from the amplitude decay and phase lag of a temperature wave traveling through the sample are derived for a flat disk sample for which only heat loss from the end surface is important, and a sample of finite diameter and length for which heat loss through the end and side surfaces must be considered. It is noted that in the case of a flat disk, measurements at a single angular frequency of the temperature wave are sufficient, while the sample of finite diameter and length requires measurements at two discrete angular frequencies. Comparison of the values of the thermal diffusivities of two lunar samples of dimensions approximately 1 x 1 x 2 cm derived by the present methods and by the Angstrom theory for a finite bar reveals them to differ by not more than 5%, and indicates that more refined data are required as the measurement theory becomes more complicated.

  10. Comparison of methods for sampling plant bugs on cotton in South Texas (2010)

    USDA-ARS?s Scientific Manuscript database

    A total of 26 cotton fields were sampled by experienced and inexperienced samplers at 3 growth stages using 5 methods to compare the most efficient and accurate method for sampling plant bugs in cotton. Each of the 5 methods had its own distinct advantages and disadvantages as a sampling method (too...

  11. A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments.

    PubMed

    Olesen, Scott W; Vora, Suhani; Techtmann, Stephen M; Fortney, Julian L; Bastidas-Oyanedel, Juan R; Rodríguez, Jorge; Hazen, Terry C; Alm, Eric J

    2016-01-01

    Many microbial ecology experiments use sequencing data to measure a community's response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samples and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method's validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of "bottle effects".

  12. A random spatial sampling method in a rural developing nation

    Treesearch

    Michelle C. Kondo; Kent D.W. Bream; Frances K. Barg; Charles C. Branas

    2014-01-01

    Nonrandom sampling of populations in developing nations has limitations and can inaccurately estimate health phenomena, especially among hard-to-reach populations such as rural residents. However, random sampling of rural populations in developing nations can be challenged by incomplete enumeration of the base population. We describe a stratified random sampling method...

  13. Methods of biological fluids sample preparation - biogenic amines, methylxanthines, water-soluble vitamins.

    PubMed

    Płonka, Joanna

    2015-01-01

    In recent years demands on the amount of information that can be obtained from the analysis of a single sample have increased. For time and economic reasons it is necessary to examine at the same time larger number of compounds, and compounds from different groups. This can best be seen in such areas as clinical analysis. In many diseases, the best results for patients are obtained when treatment fits the individual characteristics of the patient. Dosage monitoring is important at the beginning of therapy and in the full process of treatment. In the treatment of many diseases biogenic amines (dopamine, serotonin) and methylxanthines (theophylline, theobromine, caffeine) play an important role. They are used as drugs separately or in combination with others to support and strengthen the action of other drugs - for example, the combination of caffeine and paracetamol. Vitamin supplementation may be also an integral part of the treatment process. Specification of complete sample preparation parameters for extraction of the above compounds from biological matrices has been reviewed. Particular attention was given to the preparation stage and extraction methods. This review provides universal guidance on establishing a common procedures across laboratories to facilitate the preparation and analysis of all discussed compounds. Copyright © 2014 John Wiley & Sons, Ltd.

  14. A method for analysing small samples of floral pollen for free and protein-bound amino acids.

    PubMed

    Stabler, Daniel; Power, Eileen F; Borland, Anne M; Barnes, Jeremy D; Wright, Geraldine A

    2018-02-01

    Pollen provides floral visitors with essential nutrients including proteins, lipids, vitamins and minerals. As an important nutrient resource for pollinators, including honeybees and bumblebees, pollen quality is of growing interest in assessing available nutrition to foraging bees. To date, quantifying the protein-bound amino acids in pollen has been difficult and methods rely on large amounts of pollen, typically more than 1 g. More usual is to estimate a crude protein value based on the nitrogen content of pollen, however, such methods provide no information on the distribution of essential and non-essential amino acids constituting the proteins.Here, we describe a method of microwave-assisted acid hydrolysis using low amounts of pollen that allows exploration of amino acid composition, quantified using ultra high performance liquid chromatography (UHPLC), and a back calculation to estimate the crude protein content of pollen.Reliable analysis of protein-bound and free amino acids as well as an estimation of crude protein concentration was obtained from pollen samples as low as 1 mg. Greater variation in both protein-bound and free amino acids was found in pollen sample sizes <1 mg. Due to the variability in recovery of amino acids in smaller sample sizes, we suggest a correction factor to apply to specific sample sizes of pollen in order to estimate total crude protein content.The method described in this paper will allow researchers to explore the composition of amino acids in pollen and will aid research assessing the available nutrition to pollinating animals. This method will be particularly useful in assaying the pollen of wild plants, from which it is difficult to obtain large sample weights.

  15. Sampling methods for terrestrial amphibians and reptiles.

    Treesearch

    Paul Stephen Corn; R. Bruce Bury

    1990-01-01

    Methods described for sampling amphibians and reptiles in Douglas-fir forests in the Pacific Northwest include pitfall trapping, time-constrained collecting, and surveys of coarse woody debris. The herpetofauna of this region differ in breeding and nonbreeding habitats and vagility, so that no single technique is sufficient for a community study. A combination of...

  16. Simplified sample preparation method for triclosan and methyltriclosan determination in biota and foodstuff samples.

    PubMed

    Canosa, P; Rodríguez, I; Rubí, E; Ramil, M; Cela, R

    2008-04-25

    An improved method for the determination of triclosan (TCS) and methyltriclosan (MTCS) in fish and foodstuff samples is presented. Analytes were simultaneously extracted and purified using the matrix solid-phase dispersion (MSPD) technique, and then selectively determined by gas chromatography with tandem mass spectrometry (GC-MS/MS). Several combinations of dispersants, clean-up co-sorbents and extraction solvents were tested in order to obtain lipid-free extracts and quantitative recoveries for TCS and MTCS. Under optimised conditions, 0.5 g samples were dispersed using 1.5 g of neutral silica in a mortar with a pestle, and transferred to a polypropylene cartridge containing 3 g of silica impregnated with 10% of sulphuric acid (SiO2-H2SO4, 10%, w/w). Analytes were recovered with 10 mL of dichloromethane whereas lipids were oxidized in the layer of acidic silica. The extract was concentrated to dryness and re-constituted with 1 mL of ethyl acetate. Then, a fraction of 0.5 mL was mixed with 50 microL of N-methyl-N-(tert-butyldimethylsilyl)trifluoroacetamide (MTBSTFA) and injected in the GC-MS/MS system. The developed method provided absolute recoveries between 77 and 120% for different samples spiked at the low ng g(-1) level, quantification limits in the range of 1-2 ng g(-1) and a considerable simplicity in comparison with previously developed sample preparation approaches. Experiments carried out placing sliced food samples in direct contact with TCS-treated kitchenware surfaces showed the capability of the biocide to migrate into foodstuffs.

  17. Fluidics platform and method for sample preparation and analysis

    DOEpatents

    Benner, W. Henry; Dzenitis, John M.; Bennet, William J.; Baker, Brian R.

    2014-08-19

    Herein provided are fluidics platform and method for sample preparation and analysis. The fluidics platform is capable of analyzing DNA from blood samples using amplification assays such as polymerase-chain-reaction assays and loop-mediated-isothermal-amplification assays. The fluidics platform can also be used for other types of assays and analyzes. In some embodiments, a sample in a sealed tube can be inserted directly. The following isolation, detection, and analyzes can be performed without a user's intervention. The disclosed platform may also comprises a sample preparation system with a magnetic actuator, a heater, and an air-drying mechanism, and fluid manipulation processes for extraction, washing, elution, assay assembly, assay detection, and cleaning after reactions and between samples.

  18. Method and apparatus for imaging a sample on a device

    DOEpatents

    Trulson, Mark; Stern, David; Fiekowsky, Peter; Rava, Richard; Walton, Ian; Fodor, Stephen P. A.

    2001-01-01

    A method and apparatus for imaging a sample are provided. An electromagnetic radiation source generates excitation radiation which is sized by excitation optics to a line. The line is directed at a sample resting on a support and excites a plurality of regions on the sample. Collection optics collect response radiation reflected from the sample I and image the reflected radiation. A detector senses the reflected radiation and is positioned to permit discrimination between radiation reflected from a certain focal plane in the sample and certain other planes within the sample.

  19. The effects of inference method, population sampling, and gene sampling on species tree inferences: an empirical study in slender salamanders (Plethodontidae: Batrachoseps).

    PubMed

    Jockusch, Elizabeth L; Martínez-Solano, Iñigo; Timpe, Elizabeth K

    2015-01-01

    Species tree methods are now widely used to infer the relationships among species from multilocus data sets. Many methods have been developed, which differ in whether gene and species trees are estimated simultaneously or sequentially, and in how gene trees are used to infer the species tree. While these methods perform well on simulated data, less is known about what impacts their performance on empirical data. We used a data set including five nuclear genes and one mitochondrial gene for 22 species of Batrachoseps to compare the effects of method of analysis, within-species sampling and gene sampling on species tree inferences. For this data set, the choice of inference method had the largest effect on the species tree topology. Exclusion of individual loci had large effects in *BEAST and STEM, but not in MP-EST. Different loci carried the greatest leverage in these different methods, showing that the causes of their disproportionate effects differ. Even though substantial information was present in the nuclear loci, the mitochondrial gene dominated the *BEAST species tree. This leverage is inherent to the mtDNA locus and results from its high variation and lower assumed ploidy. This mtDNA leverage may be problematic when mtDNA has undergone introgression, as is likely in this data set. By contrast, the leverage of RAG1 in STEM analyses does not reflect properties inherent to the locus, but rather results from a gene tree that is strongly discordant with all others, and is best explained by introgression between distantly related species. Within-species sampling was also important, especially in *BEAST analyses, as shown by differences in tree topology across 100 subsampled data sets. Despite the sensitivity of the species tree methods to multiple factors, five species groups, the relationships among these, and some relationships within them, are generally consistently resolved for Batrachoseps. © The Author(s) 2014. Published by Oxford University Press, on

  20. Sampling methods for amphibians in streams in the Pacific Northwest.

    Treesearch

    R. Bruce Bury; Paul Stephen Corn

    1991-01-01

    Methods describing how to sample aquatic and semiaquatic amphibians in small streams and headwater habitats in the Pacific Northwest are presented. We developed a technique that samples 10-meter stretches of selected streams, which was adequate to detect presence or absence of amphibian species and provided sample sizes statistically sufficient to compare abundance of...

  1. Comparison of DNA preservation methods for environmental bacterial community samples

    USGS Publications Warehouse

    Gray, Michael A.; Pratte, Zoe A.; Kellogg, Christina A.

    2013-01-01

    Field collections of environmental samples, for example corals, for molecular microbial analyses present distinct challenges. The lack of laboratory facilities in remote locations is common, and preservation of microbial community DNA for later study is critical. A particular challenge is keeping samples frozen in transit. Five nucleic acid preservation methods that do not require cold storage were compared for effectiveness over time and ease of use. Mixed microbial communities of known composition were created and preserved by DNAgard™, RNAlater®, DMSO–EDTA–salt (DESS), FTA® cards, and FTA Elute® cards. Automated ribosomal intergenic spacer analysis and clone libraries were used to detect specific changes in the faux communities over weeks and months of storage. A previously known bias in FTA® cards that results in lower recovery of pure cultures of Gram-positive bacteria was also detected in mixed community samples. There appears to be a uniform bias across all five preservation methods against microorganisms with high G + C DNA. Overall, the liquid-based preservatives (DNAgard™, RNAlater®, and DESS) outperformed the card-based methods. No single liquid method clearly outperformed the others, leaving method choice to be based on experimental design, field facilities, shipping constraints, and allowable cost.

  2. Detection of Salmonella enterica in Meat in Less than 5 Hours by a Low-Cost and Noncomplex Sample Preparation Method

    PubMed Central

    Hoorfar, J.; Hansen, F.; Christensen, J.; Mansdal, S.; Josefsen, M. H.

    2016-01-01

    ABSTRACT Salmonella is recognized as one of the most important foodborne bacteria and has wide health and socioeconomic impacts worldwide. Fresh pork meat is one of the main sources of Salmonella, and efficient and fast methods for detection are therefore necessary. Current methods for Salmonella detection in fresh meat usually include >16 h of culture enrichment, in a few cases <12 h, thus requiring at least two working shifts. Here, we report a rapid (<5 h) and high-throughput method for screening of Salmonella in samples from fresh pork meat, consisting of a 3-h enrichment in standard buffered peptone water and a real-time PCR-compatible sample preparation method based on filtration, centrifugation, and enzymatic digestion, followed by fast-cycling real-time PCR detection. The method was validated in an unpaired comparative study against the Nordic Committee on Food Analysis (NMKL) reference culture method 187. Pork meat samples (n = 140) were either artificially contaminated with Salmonella at 0, 1 to 10, or 10 to 100 CFU/25 g of meat or naturally contaminated. Cohen's kappa for the degree of agreement between the rapid method and the reference was 0.64, and the relative accuracy, sensitivity, and specificity for the rapid method were 81.4, 95.1, and 97.9%, respectively. The 50% limit of detections (LOD50s) were 8.8 CFU/25 g for the rapid method and 7.7 CFU/25 g for the reference method. Implementation of this method will enable faster release of Salmonella low-risk meat, providing savings for meat producers, and it will help contribute to improved food safety. IMPORTANCE While the cost of analysis and hands-on time of the presented rapid method were comparable to those of reference culture methods, the fast product release by this method can provide the meat industry with a competitive advantage. Not only will the abattoirs save costs for work hours and cold storage, but consumers and retailers will also benefit from fresher meat with a longer shelf life

  3. Detection of Salmonella enterica in Meat in Less than 5 Hours by a Low-Cost and Noncomplex Sample Preparation Method.

    PubMed

    Fachmann, M S R; Löfström, C; Hoorfar, J; Hansen, F; Christensen, J; Mansdal, S; Josefsen, M H

    2017-03-01

    Salmonella is recognized as one of the most important foodborne bacteria and has wide health and socioeconomic impacts worldwide. Fresh pork meat is one of the main sources of Salmonella , and efficient and fast methods for detection are therefore necessary. Current methods for Salmonella detection in fresh meat usually include >16 h of culture enrichment, in a few cases <12 h, thus requiring at least two working shifts. Here, we report a rapid (<5 h) and high-throughput method for screening of Salmonella in samples from fresh pork meat, consisting of a 3-h enrichment in standard buffered peptone water and a real-time PCR-compatible sample preparation method based on filtration, centrifugation, and enzymatic digestion, followed by fast-cycling real-time PCR detection. The method was validated in an unpaired comparative study against the Nordic Committee on Food Analysis (NMKL) reference culture method 187. Pork meat samples ( n = 140) were either artificially contaminated with Salmonella at 0, 1 to 10, or 10 to 100 CFU/25 g of meat or naturally contaminated. Cohen's kappa for the degree of agreement between the rapid method and the reference was 0.64, and the relative accuracy, sensitivity, and specificity for the rapid method were 81.4, 95.1, and 97.9%, respectively. The 50% limit of detections (LOD 50 s) were 8.8 CFU/25 g for the rapid method and 7.7 CFU/25 g for the reference method. Implementation of this method will enable faster release of Salmonella low-risk meat, providing savings for meat producers, and it will help contribute to improved food safety. IMPORTANCE While the cost of analysis and hands-on time of the presented rapid method were comparable to those of reference culture methods, the fast product release by this method can provide the meat industry with a competitive advantage. Not only will the abattoirs save costs for work hours and cold storage, but consumers and retailers will also benefit from fresher meat with a longer shelf life

  4. Sampling Methods and the Accredited Population in Athletic Training Education Research

    ERIC Educational Resources Information Center

    Carr, W. David; Volberding, Jennifer

    2009-01-01

    Context: We describe methods of sampling the widely-studied, yet poorly defined, population of accredited athletic training education programs (ATEPs). Objective: There are two purposes to this study; first to describe the incidence and types of sampling methods used in athletic training education research, and second to clearly define the…

  5. Estimating uncertainty in respondent-driven sampling using a tree bootstrap method.

    PubMed

    Baraff, Aaron J; McCormick, Tyler H; Raftery, Adrian E

    2016-12-20

    Respondent-driven sampling (RDS) is a network-based form of chain-referral sampling used to estimate attributes of populations that are difficult to access using standard survey tools. Although it has grown quickly in popularity since its introduction, the statistical properties of RDS estimates remain elusive. In particular, the sampling variability of these estimates has been shown to be much higher than previously acknowledged, and even methods designed to account for RDS result in misleadingly narrow confidence intervals. In this paper, we introduce a tree bootstrap method for estimating uncertainty in RDS estimates based on resampling recruitment trees. We use simulations from known social networks to show that the tree bootstrap method not only outperforms existing methods but also captures the high variability of RDS, even in extreme cases with high design effects. We also apply the method to data from injecting drug users in Ukraine. Unlike other methods, the tree bootstrap depends only on the structure of the sampled recruitment trees, not on the attributes being measured on the respondents, so correlations between attributes can be estimated as well as variability. Our results suggest that it is possible to accurately assess the high level of uncertainty inherent in RDS.

  6. A Typology of Mixed Methods Sampling Designs in Social Science Research

    ERIC Educational Resources Information Center

    Onwuegbuzie, Anthony J.; Collins, Kathleen M. T.

    2007-01-01

    This paper provides a framework for developing sampling designs in mixed methods research. First, we present sampling schemes that have been associated with quantitative and qualitative research. Second, we discuss sample size considerations and provide sample size recommendations for each of the major research designs for quantitative and…

  7. System and method for measuring fluorescence of a sample

    DOEpatents

    Riot, Vincent J

    2015-03-24

    The present disclosure provides a system and a method for measuring fluorescence of a sample. The sample may be a polymerase-chain-reaction (PCR) array, a loop-mediated-isothermal amplification array, etc. LEDs are used to excite the sample, and a photodiode is used to collect the sample's fluorescence. An electronic offset signal is used to reduce the effects of background fluorescence and the noises from the measurement system. An integrator integrates the difference between the output of the photodiode and the electronic offset signal over a given period of time. The resulting integral is then converted into digital domain for further processing and storage.

  8. Photoacoustic spectroscopy sample array vessels and photoacoustic spectroscopy methods for using the same

    DOEpatents

    Amonette, James E.; Autrey, S. Thomas; Foster-Mills, Nancy S.

    2006-02-14

    Methods and apparatus for simultaneous or sequential, rapid analysis of multiple samples by photoacoustic spectroscopy are disclosed. Particularly, a photoacoustic spectroscopy sample array vessel including a vessel body having multiple sample cells connected thereto is disclosed. At least one acoustic detector is acoustically positioned near the sample cells. Methods for analyzing the multiple samples in the sample array vessels using photoacoustic spectroscopy are provided.

  9. Sparse feature learning for instrument identification: Effects of sampling and pooling methods.

    PubMed

    Han, Yoonchang; Lee, Subin; Nam, Juhan; Lee, Kyogu

    2016-05-01

    Feature learning for music applications has recently received considerable attention from many researchers. This paper reports on the sparse feature learning algorithm for musical instrument identification, and in particular, focuses on the effects of the frame sampling techniques for dictionary learning and the pooling methods for feature aggregation. To this end, two frame sampling techniques are examined that are fixed and proportional random sampling. Furthermore, the effect of using onset frame was analyzed for both of proposed sampling methods. Regarding summarization of the feature activation, a standard deviation pooling method is used and compared with the commonly used max- and average-pooling techniques. Using more than 47 000 recordings of 24 instruments from various performers, playing styles, and dynamics, a number of tuning parameters are experimented including the analysis frame size, the dictionary size, and the type of frequency scaling as well as the different sampling and pooling methods. The results show that the combination of proportional sampling and standard deviation pooling achieve the best overall performance of 95.62% while the optimal parameter set varies among the instrument classes.

  10. Perilymph sampling from the cochlear apex: a reliable method to obtain higher purity perilymph samples from scala tympani.

    PubMed

    Salt, Alec N; Hale, Shane A; Plonkte, Stefan K R

    2006-05-15

    Measurements of drug levels in the fluids of the inner ear are required to establish kinetic parameters and to determine the influence of specific local delivery protocols. For most substances, this requires cochlear fluids samples to be obtained for analysis. When auditory function is of primary interest, the drug level in the perilymph of scala tympani (ST) is most relevant, since drug in this scala has ready access to the auditory sensory cells. In many prior studies, ST perilymph samples have been obtained from the basal turn, either by aspiration through the round window membrane (RWM) or through an opening in the bony wall. A number of studies have demonstrated that such samples are likely to be contaminated with cerebrospinal fluid (CSF). CSF enters the basal turn of ST through the cochlear aqueduct when the bony capsule is perforated or when fluid is aspirated. The degree of sample contamination has, however, not been widely appreciated. Recent studies have shown that perilymph samples taken through the round window membrane are highly contaminated with CSF, with samples greater than 2microL in volume containing more CSF than perilymph. In spite of this knowledge, many groups continue to sample from the base of the cochlea, as it is a well-established method. We have developed an alternative, technically simple method to increase the proportion of ST perilymph in a fluid sample. The sample is taken from the apex of the cochlea, a site that is distant from the cochlear aqueduct. A previous problem with sampling through a perforation in the bone was that the native perilymph rapidly leaked out driven by CSF pressure and was lost to the middle ear space. We therefore developed a procedure to collect all the fluid that emerged from the perforated apex after perforation. We evaluated the method using a marker ion trimethylphenylammonium (TMPA). TMPA was applied to the perilymph of guinea pigs either by RW irrigation or by microinjection into the apical turn. The

  11. Perilymph Sampling from the Cochlear Apex: A Reliable Method to Obtain Higher Purity Perilymph Samples from Scala Tympani

    PubMed Central

    Salt, Alec N.; Hale, Shane A.; Plontke, Stefan K. R.

    2006-01-01

    Measurements of drug levels in the fluids of the inner ear are required to establish kinetic parameters and to determine the influence of specific local delivery protocols. For most substances, this requires cochlear fluids samples to be obtained for analysis. When auditory function is of primary interest, the drug level in the perilymph of scala tympani (ST) is most relevant, since drug in this scala has ready access to the auditory sensory cells. In many prior studies, ST perilymph samples have been obtained from the basal turn, either by aspiration through the round window membrane (RWM) or through an opening in the bony wall. A number of studies have demonstrated that such samples are likely to be contaminated with cerebrospinal fluid (CSF). CSF enters the basal turn of ST through the cochlear aqueduct when the bony capsule is perforated or when fluid is aspirated. The degree of sample contamination has, however, not been widely appreciated. Recent studies have shown that perilymph samples taken through the round window membrane are highly contaminated with CSF, with samples greater than 2 μL in volume containing more CSF than perilymph. In spite of this knowledge, many groups continue to sample from the base of the cochlea, as it is a well-established method. We have developed an alternative, technically simple method to increase the proportion of ST perilymph in a fluid sample. The sample is taken from the apex of the cochlea, a site that is distant from the cochlear aqueduct. A previous problem with sampling through a perforation in the bone was that the native perilymph rapidly leaked out driven by CSF pressure and was lost to the middle ear space. We therefore developed a procedure to collect all the fluid that emerged from the perforated apex after perforation. We evaluated the method using a marker ion trimethylphenylammonium (TMPA). TMPA was applied to the perilymph of guinea pigs either by RW irrigation or by microinjection into the apical turn. The

  12. Sensitive spectrophotometric determination of Co(II) using dispersive liquid-liquid micro-extraction method in soil samples.

    PubMed

    Hasanpour, Foroozan; Hadadzadeh, Hassan; Taei, Masoumeh; Nekouei, Mohsen; Mozafari, Elmira

    2016-05-01

    Analytical performance of conventional spectrophotometer was developed by coupling of effective dispersive liquid-liquid micro-extraction method with spectrophotometric determination for ultra-trace determination of cobalt. The method was based on the formation of Co(II)-alpha-benzoin oxime complex and its extraction using a dispersive liquid-liquid micro-extraction technique. During the present work, several important variables such as pH, ligand concentration, amount and type of dispersive, and extracting solvent were optimized. It was found that the crucial factor for the Co(II)-alpha benzoin oxime complex formation is the pH of the alkaline alcoholic medium. Under the optimized condition, the calibration graph was linear in the ranges of 1.0-110 μg L(-1) with the detection limit (S/N = 3) of 0.5 μg L(-1). The preconcentration operation of 25 mL of sample gave enhancement factor of 75. The proposed method was applied for determination of Co(II) in soil samples.

  13. Survey research with a random digit dial national mobile phone sample in Ghana: Methods and sample quality

    PubMed Central

    Sefa, Eunice; Adimazoya, Edward Akolgo; Yartey, Emmanuel; Lenzi, Rachel; Tarpo, Cindy; Heward-Mills, Nii Lante; Lew, Katherine; Ampeh, Yvonne

    2018-01-01

    Introduction Generating a nationally representative sample in low and middle income countries typically requires resource-intensive household level sampling with door-to-door data collection. High mobile phone penetration rates in developing countries provide new opportunities for alternative sampling and data collection methods, but there is limited information about response rates and sample biases in coverage and nonresponse using these methods. We utilized data from an interactive voice response, random-digit dial, national mobile phone survey in Ghana to calculate standardized response rates and assess representativeness of the obtained sample. Materials and methods The survey methodology was piloted in two rounds of data collection. The final survey included 18 demographic, media exposure, and health behavior questions. Call outcomes and response rates were calculated according to the American Association of Public Opinion Research guidelines. Sample characteristics, productivity, and costs per interview were calculated. Representativeness was assessed by comparing data to the Ghana Demographic and Health Survey and the National Population and Housing Census. Results The survey was fielded during a 27-day period in February-March 2017. There were 9,469 completed interviews and 3,547 partial interviews. Response, cooperation, refusal, and contact rates were 31%, 81%, 7%, and 39% respectively. Twenty-three calls were dialed to produce an eligible contact: nonresponse was substantial due to the automated calling system and dialing of many unassigned or non-working numbers. Younger, urban, better educated, and male respondents were overrepresented in the sample. Conclusions The innovative mobile phone data collection methodology yielded a large sample in a relatively short period. Response rates were comparable to other surveys, although substantial coverage bias resulted from fewer women, rural, and older residents completing the mobile phone survey in

  14. A multi-threshold sampling method for TOF-PET signal processing

    NASA Astrophysics Data System (ADS)

    Kim, H.; Kao, C. M.; Xie, Q.; Chen, C. T.; Zhou, L.; Tang, F.; Frisch, H.; Moses, W. W.; Choong, W. S.

    2009-04-01

    As an approach to realizing all-digital data acquisition for positron emission tomography (PET), we have previously proposed and studied a multi-threshold sampling method to generate samples of a PET event waveform with respect to a few user-defined amplitudes. In this sampling scheme, one can extract both the energy and timing information for an event. In this paper, we report our prototype implementation of this sampling method and the performance results obtained with this prototype. The prototype consists of two multi-threshold discriminator boards and a time-to-digital converter (TDC) board. Each of the multi-threshold discriminator boards takes one input and provides up to eight threshold levels, which can be defined by users, for sampling the input signal. The TDC board employs the CERN HPTDC chip that determines the digitized times of the leading and falling edges of the discriminator output pulses. We connect our prototype electronics to the outputs of two Hamamatsu R9800 photomultiplier tubes (PMTs) that are individually coupled to a 6.25×6.25×25 mm3 LSO crystal. By analyzing waveform samples generated by using four thresholds, we obtain a coincidence timing resolution of about 340 ps and an ˜18% energy resolution at 511 keV. We are also able to estimate the decay-time constant from the resulting samples and obtain a mean value of 44 ns with an ˜9 ns FWHM. In comparison, using digitized waveforms obtained at a 20 GSps sampling rate for the same LSO/PMT modules we obtain ˜300 ps coincidence timing resolution, ˜14% energy resolution at 511 keV, and ˜5 ns FWHM for the estimated decay-time constant. Details of the results on the timing and energy resolutions by using the multi-threshold method indicate that it is a promising approach for implementing digital PET data acquisition.

  15. A Mixed Methods Sampling Methodology for a Multisite Case Study

    ERIC Educational Resources Information Center

    Sharp, Julia L.; Mobley, Catherine; Hammond, Cathy; Withington, Cairen; Drew, Sam; Stringfield, Sam; Stipanovic, Natalie

    2012-01-01

    The flexibility of mixed methods research strategies makes such approaches especially suitable for multisite case studies. Yet the utilization of mixed methods to select sites for these studies is rarely reported. The authors describe their pragmatic mixed methods approach to select a sample for their multisite mixed methods case study of a…

  16. 7 CFR 51.308 - Methods of sampling and calculation of percentages.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... Grades of Apples Methods of Sampling and Calculation of Percentages § 51.308 Methods of sampling and... weigh ten pounds or less, or in any container where the minimum diameter of the smallest apple does not vary more than 1/2 inch from the minimum diameter of the largest apple, percentages shall be calculated...

  17. 7 CFR 51.308 - Methods of sampling and calculation of percentages.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... Grades of Apples Methods of Sampling and Calculation of Percentages § 51.308 Methods of sampling and... weigh ten pounds or less, or in any container where the minimum diameter of the smallest apple does not vary more than 1/2 inch from the minimum diameter of the largest apple, percentages shall be calculated...

  18. CHARACTERIZATION OF HAZARDOUS WASTE SITES, A METHODS MANUAL. VOLUME 2. AVAILABLE SAMPLING METHODS (SECOND EDITION)

    EPA Science Inventory

    Investigations at hazardous waste sites and sites of chemical spills often require on-site measurements and sampling activities to assess the type and extent of contamination. This document is a compilation of sampling methods and materials suitable to address most needs that ari...

  19. [Standard sample preparation method for quick determination of trace elements in plastic].

    PubMed

    Yao, Wen-Qing; Zong, Rui-Long; Zhu, Yong-Fa

    2011-08-01

    Reference sample was prepared by masterbatch method, containing heavy metals with known concentration of electronic information products (plastic), the repeatability and precision were determined, and reference sample preparation procedures were established. X-Ray fluorescence spectroscopy (XRF) analysis method was used to determine the repeatability and uncertainty in the analysis of the sample of heavy metals and bromine element. The working curve and the metrical methods for the reference sample were carried out. The results showed that the use of the method in the 200-2000 mg x kg(-1) concentration range for Hg, Pb, Cr and Br elements, and in the 20-200 mg x kg(-1) range for Cd elements, exhibited a very good linear relationship, and the repeatability of analysis methods for six times is good. In testing the circuit board ICB288G and ICB288 from the Mitsubishi Heavy Industry Company, results agreed with the recommended values.

  20. Evaluation of a Class of Simple and Effective Uncertainty Methods for Sparse Samples of Random Variables and Functions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Romero, Vicente; Bonney, Matthew; Schroeder, Benjamin

    When very few samples of a random quantity are available from a source distribution of unknown shape, it is usually not possible to accurately infer the exact distribution from which the data samples come. Under-estimation of important quantities such as response variance and failure probabilities can result. For many engineering purposes, including design and risk analysis, we attempt to avoid under-estimation with a strategy to conservatively estimate (bound) these types of quantities -- without being overly conservative -- when only a few samples of a random quantity are available from model predictions or replicate experiments. This report examines a classmore » of related sparse-data uncertainty representation and inference approaches that are relatively simple, inexpensive, and effective. Tradeoffs between the methods' conservatism, reliability, and risk versus number of data samples (cost) are quantified with multi-attribute metrics use d to assess method performance for conservative estimation of two representative quantities: central 95% of response; and 10 -4 probability of exceeding a response threshold in a tail of the distribution. Each method's performance is characterized with 10,000 random trials on a large number of diverse and challenging distributions. The best method and number of samples to use in a given circumstance depends on the uncertainty quantity to be estimated, the PDF character, and the desired reliability of bounding the true value. On the basis of this large data base and study, a strategy is proposed for selecting the method and number of samples for attaining reasonable credibility levels in bounding these types of quantities when sparse samples of random variables or functions are available from experiments or simulations.« less

  1. Flagging versus dragging as sampling methods for nymphal Ixodes scapularis (Acari: Ixodidae)

    USGS Publications Warehouse

    Rulison, Eric L.; Kuczaj, Isis; Pang, Genevieve; Hickling, Graham J.; Tsao, Jean I.; Ginsberg, Howard S.

    2013-01-01

    The nymphal stage of the blacklegged tick, Ixodes scapularis (Acari: Ixodidae), is responsible for most transmission of Borrelia burgdorferi, the etiologic agent of Lyme disease, to humans in North America. From 2010 to fall of 2012, we compared two commonly used techniques, flagging and dragging, as sampling methods for nymphal I. scapularis at three sites, each with multiple sampling arrays (grids), in the eastern and central United States. Flagging and dragging collected comparable numbers of nymphs, with no consistent differences between methods. Dragging collected more nymphs than flagging in some samples, but these differences were not consistent among sites or sampling years. The ratio of nymphs collected by flagging vs dragging was not significantly related to shrub density, so habitat type did not have a strong effect on the relative efficacy of these methods. Therefore, although dragging collected more ticks in a few cases, the numbers collected by each method were so variable that neither technique had a clear advantage for sampling nymphal I. scapularis.

  2. Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett's Acceptance Ratio and Enveloping Distribution Sampling Methods.

    PubMed

    König, Gerhard; Miller, Benjamin T; Boresch, Stefan; Wu, Xiongwu; Brooks, Bernard R

    2012-10-09

    One of the key requirements for the accurate calculation of free energy differences is proper sampling of conformational space. Especially in biological applications, molecular dynamics simulations are often confronted with rugged energy surfaces and high energy barriers, leading to insufficient sampling and, in turn, poor convergence of the free energy results. In this work, we address this problem by employing enhanced sampling methods. We explore the possibility of using self-guided Langevin dynamics (SGLD) to speed up the exploration process in free energy simulations. To obtain improved free energy differences from such simulations, it is necessary to account for the effects of the bias due to the guiding forces. We demonstrate how this can be accomplished for the Bennett's acceptance ratio (BAR) and the enveloping distribution sampling (EDS) methods. While BAR is considered among the most efficient methods available for free energy calculations, the EDS method developed by Christ and van Gunsteren is a promising development that reduces the computational costs of free energy calculations by simulating a single reference state. To evaluate the accuracy of both approaches in connection with enhanced sampling, EDS was implemented in CHARMM. For testing, we employ benchmark systems with analytical reference results and the mutation of alanine to serine. We find that SGLD with reweighting can provide accurate results for BAR and EDS where conventional molecular dynamics simulations fail. In addition, we compare the performance of EDS with other free energy methods. We briefly discuss the implications of our results and provide practical guidelines for conducting free energy simulations with SGLD.

  3. Photoacoustic spectroscopy sample array vessel and photoacoustic spectroscopy method for using the same

    DOEpatents

    Amonette, James E.; Autrey, S. Thomas; Foster-Mills, Nancy S.; Green, David

    2005-03-29

    Methods and apparatus for analysis of multiple samples by photoacoustic spectroscopy are disclosed. Particularly, a photoacoustic spectroscopy sample array vessel including a vessel body having multiple sample cells connected thereto is disclosed. At least one acoustic detector is acoustically coupled with the vessel body. Methods for analyzing the multiple samples in the sample array vessels using photoacoustic spectroscopy are provided.

  4. Some refinements on the comparison of areal sampling methods via simulation

    Treesearch

    Jeffrey Gove

    2017-01-01

    The design of forest inventories and development of new sampling methods useful in such inventories normally have a two-fold target of design unbiasedness and minimum variance in mind. Many considerations such as costs go into the choices of sampling method for operational and other levels of inventory. However, the variance in terms of meeting a specified level of...

  5. An investigative comparison of purging and non-purging groundwater sampling methods in Karoo aquifer monitoring wells

    NASA Astrophysics Data System (ADS)

    Gomo, M.; Vermeulen, D.

    2015-03-01

    An investigation was conducted to statistically compare the influence of non-purging and purging groundwater sampling methods on analysed inorganic chemistry parameters and calculated saturation indices. Groundwater samples were collected from 15 monitoring wells drilled in Karoo aquifers before and after purging for the comparative study. For the non-purging method, samples were collected from groundwater flow zones located in the wells using electrical conductivity (EC) profiling. The two data sets of non-purged and purged groundwater samples were analysed for inorganic chemistry parameters at the Institute of Groundwater Studies (IGS) laboratory of the Free University in South Africa. Saturation indices for mineral phases that were found in the data base of PHREEQC hydrogeochemical model were calculated for each data set. Four one-way ANOVA tests were conducted using Microsoft excel 2007 to investigate if there is any statistically significant difference between: (1) all inorganic chemistry parameters measured in the non-purged and purged groundwater samples per each specific well, (2) all mineral saturation indices calculated for the non-purged and purged groundwater samples per each specific well, (3) individual inorganic chemistry parameters measured in the non-purged and purged groundwater samples across all wells and (4) Individual mineral saturation indices calculated for non-purged and purged groundwater samples across all wells. For all the ANOVA tests conducted, the calculated alpha values (p) are greater than 0.05 (significance level) and test statistic (F) is less than the critical value (Fcrit) (F < Fcrit). The results imply that there was no statistically significant difference between the two data sets. With a 95% confidence, it was therefore concluded that the variance between groups was rather due to random chance and not to the influence of the sampling methods (tested factor). It is therefore be possible that in some hydrogeologic conditions

  6. The Precision Efficacy Analysis for Regression Sample Size Method.

    ERIC Educational Resources Information Center

    Brooks, Gordon P.; Barcikowski, Robert S.

    The general purpose of this study was to examine the efficiency of the Precision Efficacy Analysis for Regression (PEAR) method for choosing appropriate sample sizes in regression studies used for precision. The PEAR method, which is based on the algebraic manipulation of an accepted cross-validity formula, essentially uses an effect size to…

  7. Comparison of four sampling methods for the detection of Salmonella in broiler litter.

    PubMed

    Buhr, R J; Richardson, L J; Cason, J A; Cox, N A; Fairchild, B D

    2007-01-01

    Experiments were conducted to compare litter sampling methods for the detection of Salmonella. In experiment 1, chicks were challenged orally with a suspension of naladixic acid-resistant Salmonella and wing banded, and additional nonchallenged chicks were placed into each of 2 challenge pens. Nonchallenged chicks were placed into each nonchallenge pen located adjacent to the challenge pens. At 7, 8, 10, and 11 wk of age the litter was sampled using 4 methods: fecal droppings, litter grab, drag swab, and sock. For the challenge pens, Salmonella-positive samples were detected in 3 of 16 fecal samples, 6 of 16 litter grab samples, 7 of 16 drag swabs samples, and 7 of 16 sock samples. Samples from the nonchallenge pens were Salmonella positive in 2 of 16 litter grab samples, 9 of 16 drag swab samples, and 9 of 16 sock samples. In experiment 2, chicks were challenged with Salmonella, and the litter in the challenge and adjacent nonchallenge pens were sampled at 4, 6, and 8 wk of age with broilers remaining in all pens. For the challenge pens, Salmonella was detected in 10 of 36 fecal samples, 20 of 36 litter grab samples, 14 of 36 drag swab samples, and 26 of 36 sock samples. Samples from the adjacent nonchallenge pens were positive for Salmonella in 6 of 36 fecal droppings samples, 4 of 36 litter grab samples, 7 of 36 drag swab samples, and 19 of 36 sock samples. Sock samples had the highest rates of Salmonella detection. In experiment 3, the litter from a Salmonella-challenged flock was sampled at 7, 8, and 9 wk by socks and drag swabs. In addition, comparisons with drag swabs that were stepped on during sampling were made. Both socks (24 of 36, 67%) and drag swabs that were stepped on (25 of 36, 69%) showed significantly more Salmonella-positive samples than the traditional drag swab method (16 of 36, 44%). Drag swabs that were stepped on had comparable Salmonella detection level to that for socks. Litter sampling methods that incorporate stepping on the sample

  8. Determination of Oebalus pugnax (Hemiptera: Pentatomidae) spatial pattern in rice and development of visual sampling methods and population sampling plans.

    PubMed

    Espino, L; Way, M O; Wilson, L T

    2008-02-01

    Commercial rice, Oryza sativa L., fields in southeastern Texas were sampled during 2003 and 2004, and visual samples were compared with sweep net samples. Fields were sampled at different stages of panicle development, times of day, and by different operators. Significant differences were found between perimeter and within field sweep net samples, indicating that samples taken 9 m from the field margin overestimate within field Oebalus pugnax (F.) (Hemiptera: Pentatomidae) populations. Time of day did not significantly affect the number of O. pugnax caught with the sweep net; however, there was a trend to capture more insects during morning than afternoon. For all sampling methods evaluated during this study, O. pugnax was found to have an aggregated spatial pattern at most densities. When comparing sweep net with visual sampling methods, one sweep of the "long stick" and two sweeps of the "sweep stick" correlated well with the sweep net (r2 = 0.639 and r2 = 0.815, respectively). This relationship was not affected by time of day of sampling, stage of panicle development, type of planting or operator. Relative cost-reliability, which incorporates probability of adoption, indicates the visual methods are more cost-reliable than the sweep net for sampling O.

  9. Method and apparatus for sampling low-yield wells

    DOEpatents

    Last, George V.; Lanigan, David C.

    2003-04-15

    An apparatus and method for collecting a sample from a low-yield well or perched aquifer includes a pump and a controller responsive to water level sensors for filling a sample reservoir. The controller activates the pump to fill the reservoir when the water level in the well reaches a high level as indicated by the sensor. The controller deactivates the pump when the water level reaches a lower level as indicated by the sensors. The pump continuously activates and deactivates the pump until the sample reservoir is filled with a desired volume, as indicated by a reservoir sensor. At the beginning of each activation cycle, the controller optionally can select to purge an initial quantity of water prior to filling the sample reservoir. The reservoir can be substantially devoid of air and the pump is a low volumetric flow rate pump. Both the pump and the reservoir can be located either inside or outside the well.

  10. On the Exploitation of Sensitivity Derivatives for Improving Sampling Methods

    NASA Technical Reports Server (NTRS)

    Cao, Yanzhao; Hussaini, M. Yousuff; Zang, Thomas A.

    2003-01-01

    Many application codes, such as finite-element structural analyses and computational fluid dynamics codes, are capable of producing many sensitivity derivatives at a small fraction of the cost of the underlying analysis. This paper describes a simple variance reduction method that exploits such inexpensive sensitivity derivatives to increase the accuracy of sampling methods. Three examples, including a finite-element structural analysis of an aircraft wing, are provided that illustrate an order of magnitude improvement in accuracy for both Monte Carlo and stratified sampling schemes.

  11. Method for using polarization gating to measure a scattering sample

    DOEpatents

    Baba, Justin S.

    2015-08-04

    Described herein are systems, devices, and methods facilitating optical characterization of scattering samples. A polarized optical beam can be directed to pass through a sample to be tested. The optical beam exiting the sample can then be analyzed to determine its degree of polarization, from which other properties of the sample can be determined. In some cases, an apparatus can include a source of an optical beam, an input polarizer, a sample, an output polarizer, and a photodetector. In some cases, a signal from a photodetector can be processed through attenuation, variable offset, and variable gain.

  12. Sampling and sample processing in pesticide residue analysis.

    PubMed

    Lehotay, Steven J; Cook, Jo Marie

    2015-05-13

    Proper sampling and sample processing in pesticide residue analysis of food and soil have always been essential to obtain accurate results, but the subject is becoming a greater concern as approximately 100 mg test portions are being analyzed with automated high-throughput analytical methods by agrochemical industry and contract laboratories. As global food trade and the importance of monitoring increase, the food industry and regulatory laboratories are also considering miniaturized high-throughput methods. In conjunction with a summary of the symposium "Residues in Food and Feed - Going from Macro to Micro: The Future of Sample Processing in Residue Analytical Methods" held at the 13th IUPAC International Congress of Pesticide Chemistry, this is an opportune time to review sampling theory and sample processing for pesticide residue analysis. If collected samples and test portions do not adequately represent the actual lot from which they came and provide meaningful results, then all costs, time, and efforts involved in implementing programs using sophisticated analytical instruments and techniques are wasted and can actually yield misleading results. This paper is designed to briefly review the often-neglected but crucial topic of sample collection and processing and put the issue into perspective for the future of pesticide residue analysis. It also emphasizes that analysts should demonstrate the validity of their sample processing approaches for the analytes/matrices of interest and encourages further studies on sampling and sample mass reduction to produce a test portion.

  13. Method and apparatus for imaging a sample on a device

    DOEpatents

    Trulson, Mark; Stern, David; Fiekowsky, Peter; Rava, Richard; Walton, Ian; Fodor, Stephen P. A.

    1996-01-01

    The present invention provides methods and systems for detecting a labeled marker on a sample located on a support. The imaging system comprises a body for immobilizing the support, an excitation radiation source and excitation optics to generate and direct the excitation radiation at the sample. In response, labeled material on the sample emits radiation which has a wavelength that is different from the excitation wavelength, which radiation is collected by collection optics and imaged onto a detector which generates an image of the sample.

  14. A method for sampling waste corn

    USGS Publications Warehouse

    Frederick, R.B.; Klaas, E.E.; Baldassarre, G.A.; Reinecke, K.J.

    1984-01-01

    Corn had become one of the most important wildlife food in the United States. It is eaten by a wide variety of animals, including white-tailed deer (Odocoileus virginianus ), raccoon (Procyon lotor ), ring-necked pheasant (Phasianus colchicus , wild turkey (Meleagris gallopavo ), and many species of aquatic birds. Damage to unharvested crops had been documented, but many birds and mammals eat waste grain after harvest and do not conflict with agriculture. A good method for measuring waste-corn availability can be essential to studies concerning food density and food and feeding habits of field-feeding wildlife. Previous methods were developed primarily for approximating losses due to harvest machinery. In this paper, a method is described for estimating the amount of waste corn potentially available to wildlife. Detection of temporal changes in food availability and differences caused by agricultural operations (e.g., recently harvested stubble fields vs. plowed fields) are discussed.

  15. A Method for Extracting Important Segments from Documents Using Support Vector Machines

    NASA Astrophysics Data System (ADS)

    Suzuki, Daisuke; Utsumi, Akira

    In this paper we propose an extraction-based method for automatic summarization. The proposed method consists of two processes: important segment extraction and sentence compaction. The process of important segment extraction classifies each segment in a document as important or not by Support Vector Machines (SVMs). The process of sentence compaction then determines grammatically appropriate portions of a sentence for a summary according to its dependency structure and the classification result by SVMs. To test the performance of our method, we conducted an evaluation experiment using the Text Summarization Challenge (TSC-1) corpus of human-prepared summaries. The result was that our method achieved better performance than a segment-extraction-only method and the Lead method, especially for sentences only a part of which was included in human summaries. Further analysis of the experimental results suggests that a hybrid method that integrates sentence extraction with segment extraction may generate better summaries.

  16. Predictive Sampling of Rare Conformational Events in Aqueous Solution: Designing a Generalized Orthogonal Space Tempering Method.

    PubMed

    Lu, Chao; Li, Xubin; Wu, Dongsheng; Zheng, Lianqing; Yang, Wei

    2016-01-12

    In aqueous solution, solute conformational transitions are governed by intimate interplays of the fluctuations of solute-solute, solute-water, and water-water interactions. To promote molecular fluctuations to enhance sampling of essential conformational changes, a common strategy is to construct an expanded Hamiltonian through a series of Hamiltonian perturbations and thereby broaden the distribution of certain interactions of focus. Due to a lack of active sampling of configuration response to Hamiltonian transitions, it is challenging for common expanded Hamiltonian methods to robustly explore solvent mediated rare conformational events. The orthogonal space sampling (OSS) scheme, as exemplified by the orthogonal space random walk and orthogonal space tempering methods, provides a general framework for synchronous acceleration of slow configuration responses. To more effectively sample conformational transitions in aqueous solution, in this work, we devised a generalized orthogonal space tempering (gOST) algorithm. Specifically, in the Hamiltonian perturbation part, a solvent-accessible-surface-area-dependent term is introduced to implicitly perturb near-solute water-water fluctuations; more importantly in the orthogonal space response part, the generalized force order parameter is generalized as a two-dimension order parameter set, in which essential solute-solvent and solute-solute components are separately treated. The gOST algorithm is evaluated through a molecular dynamics simulation study on the explicitly solvated deca-alanine (Ala10) peptide. On the basis of a fully automated sampling protocol, the gOST simulation enabled repetitive folding and unfolding of the solvated peptide within a single continuous trajectory and allowed for detailed constructions of Ala10 folding/unfolding free energy surfaces. The gOST result reveals that solvent cooperative fluctuations play a pivotal role in Ala10 folding/unfolding transitions. In addition, our assessment

  17. Adaptive Annealed Importance Sampling for Multimodal Posterior Exploration and Model Selection with Application to Extrasolar Planet Detection

    NASA Astrophysics Data System (ADS)

    Liu, Bin

    2014-07-01

    We describe an algorithm that can adaptively provide mixture summaries of multimodal posterior distributions. The parameter space of the involved posteriors ranges in size from a few dimensions to dozens of dimensions. This work was motivated by an astrophysical problem called extrasolar planet (exoplanet) detection, wherein the computation of stochastic integrals that are required for Bayesian model comparison is challenging. The difficulty comes from the highly nonlinear models that lead to multimodal posterior distributions. We resort to importance sampling (IS) to estimate the integrals, and thus translate the problem to be how to find a parametric approximation of the posterior. To capture the multimodal structure in the posterior, we initialize a mixture proposal distribution and then tailor its parameters elaborately to make it resemble the posterior to the greatest extent possible. We use the effective sample size (ESS) calculated based on the IS draws to measure the degree of approximation. The bigger the ESS is, the better the proposal resembles the posterior. A difficulty within this tailoring operation lies in the adjustment of the number of mixing components in the mixture proposal. Brute force methods just preset it as a large constant, which leads to an increase in the required computational resources. We provide an iterative delete/merge/add process, which works in tandem with an expectation-maximization step to tailor such a number online. The efficiency of our proposed method is tested via both simulation studies and real exoplanet data analysis.

  18. A novel analysis method for paired-sample microbial ecology experiments

    DOE PAGES

    Olesen, Scott W.; Vora, Suhani; Techtmann, Stephen M.; ...

    2016-05-06

    Many microbial ecology experiments use sequencing data to measure a community s response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samplesmore » and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method s validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Furthermore, our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of bottle effects .« less

  19. Comparison of DNA preservation methods for environmental bacterial community samples.

    PubMed

    Gray, Michael A; Pratte, Zoe A; Kellogg, Christina A

    2013-02-01

    Field collections of environmental samples, for example corals, for molecular microbial analyses present distinct challenges. The lack of laboratory facilities in remote locations is common, and preservation of microbial community DNA for later study is critical. A particular challenge is keeping samples frozen in transit. Five nucleic acid preservation methods that do not require cold storage were compared for effectiveness over time and ease of use. Mixed microbial communities of known composition were created and preserved by DNAgard(™), RNAlater(®), DMSO-EDTA-salt (DESS), FTA(®) cards, and FTA Elute(®) cards. Automated ribosomal intergenic spacer analysis and clone libraries were used to detect specific changes in the faux communities over weeks and months of storage. A previously known bias in FTA(®) cards that results in lower recovery of pure cultures of Gram-positive bacteria was also detected in mixed community samples. There appears to be a uniform bias across all five preservation methods against microorganisms with high G + C DNA. Overall, the liquid-based preservatives (DNAgard(™), RNAlater(®), and DESS) outperformed the card-based methods. No single liquid method clearly outperformed the others, leaving method choice to be based on experimental design, field facilities, shipping constraints, and allowable cost. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  20. A novel analysis method for paired-sample microbial ecology experiments

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Olesen, Scott W.; Vora, Suhani; Techtmann, Stephen M.

    Many microbial ecology experiments use sequencing data to measure a community s response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samplesmore » and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method s validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Furthermore, our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of bottle effects .« less

  1. Inverse supercritical fluid extraction as a sample preparation method for the analysis of the nanoparticle content in sunscreen agents.

    PubMed

    Müller, David; Cattaneo, Stefano; Meier, Florian; Welz, Roland; de Vries, Tjerk; Portugal-Cohen, Meital; Antonio, Diana C; Cascio, Claudia; Calzolai, Luigi; Gilliland, Douglas; de Mello, Andrew

    2016-04-01

    We demonstrate the use of inverse supercritical carbon dioxide (scCO2) extraction as a novel method of sample preparation for the analysis of complex nanoparticle-containing samples, in our case a model sunscreen agent with titanium dioxide nanoparticles. The sample was prepared for analysis in a simplified process using a lab scale supercritical fluid extraction system. The residual material was easily dispersed in an aqueous solution and analyzed by Asymmetrical Flow Field-Flow Fractionation (AF4) hyphenated with UV- and Multi-Angle Light Scattering detection. The obtained results allowed an unambiguous determination of the presence of nanoparticles within the sample, with almost no background from the matrix itself, and showed that the size distribution of the nanoparticles is essentially maintained. These results are especially relevant in view of recently introduced regulatory requirements concerning the labeling of nanoparticle-containing products. The novel sample preparation method is potentially applicable to commercial sunscreens or other emulsion-based cosmetic products and has important ecological advantages over currently used sample preparation techniques involving organic solvents. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Probability Sampling Method for a Hidden Population Using Respondent-Driven Sampling: Simulation for Cancer Survivors.

    PubMed

    Jung, Minsoo

    2015-01-01

    When there is no sampling frame within a certain group or the group is concerned that making its population public would bring social stigma, we say the population is hidden. It is difficult to approach this kind of population survey-methodologically because the response rate is low and its members are not quite honest with their responses when probability sampling is used. The only alternative known to address the problems caused by previous methods such as snowball sampling is respondent-driven sampling (RDS), which was developed by Heckathorn and his colleagues. RDS is based on a Markov chain, and uses the social network information of the respondent. This characteristic allows for probability sampling when we survey a hidden population. We verified through computer simulation whether RDS can be used on a hidden population of cancer survivors. According to the simulation results of this thesis, the chain-referral sampling of RDS tends to minimize as the sample gets bigger, and it becomes stabilized as the wave progresses. Therefore, it shows that the final sample information can be completely independent from the initial seeds if a certain level of sample size is secured even if the initial seeds were selected through convenient sampling. Thus, RDS can be considered as an alternative which can improve upon both key informant sampling and ethnographic surveys, and it needs to be utilized for various cases domestically as well.

  3. Determination of phenolic priority pollutants utilizing permeation sampling method

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhang, Guozheng.

    1990-01-01

    A passive permeation sampling method for the determination of phenolic priority pollutants in water was developed. Phenols in an aqueous solution permeate a polymeric membrane and are collected on a solid adsorbent in a sampling device. Both solvent and thermal desorption techniques were employed to recovery phenolic pollutants collected. In the solvent desorption, phenolic compounds collected on the XAD-7 resin, and then desorbed by acetonitrile. In the thermal desorption, phenolic compounds collected on Tenax-TA were recovered thermally, Separation and quantification is achieved by a SPB-5 capillary column gas chromatography using a flame ionization detector. There are linear relationships between themore » amount of phenolic compounds collected and the products of the exposure times and concentrations over the range from 5 ppb to 20 ppm with precisions no worse than 13%. The permeation rates of the phenolic pollutants depend upon the exposure temperature, solution pH and membrane area. Samples collected can be stored for up to two weeks without loss. This method provides a simple, convenient and inexpensive way for monitoring the time-weighted-average concentration without the use of a pumping system. An automated sampler which combines the permeation and the thermal desorption techniques together was also developed for water sample obtained from grab sampling. The on-line setup provides a high degree of automation. Detection limits at 10 ppb can be achieved using this sampler.« less

  4. Rock sampling. [method for controlling particle size distribution

    NASA Technical Reports Server (NTRS)

    Blum, P. (Inventor)

    1971-01-01

    A method for sampling rock and other brittle materials and for controlling resultant particle sizes is described. The method involves cutting grooves in the rock surface to provide a grouping of parallel ridges and subsequently machining the ridges to provide a powder specimen. The machining step may comprise milling, drilling, lathe cutting or the like; but a planing step is advantageous. Control of the particle size distribution is effected primarily by changing the height and width of these ridges. This control exceeds that obtainable by conventional grinding.

  5. Method for producing a thin sample band in a microchannel device

    DOEpatents

    Griffiths, Stewart K [Livermore, CA; Nilson, Robert H [Cardiff, CA

    2004-08-03

    The present invention improves the performance of microchannel systems for chemical and biological synthesis and analysis by providing a method and apparatus for producing a thin band of a species sample. Thin sample bands improve the resolution of microchannel separation processes, as well as many other processes requiring precise control of sample size and volume. The new method comprises a series of steps in which a species sample is manipulated by controlled transport through a junction formed at the intersection of four or more channels. A sample is first inserted into the end of one of these channels in the vicinity of the junction. Next, this sample is thinned by transport across the junction one or more times. During these thinning steps, flow enters the junction through one of the channels and exists through those remaining, providing a divergent flow field that progressively stretches and thins the band with each traverse of the junction. The thickness of the resulting sample band may be smaller than the channel width. Moreover, the thickness of the band may be varied and controlled by altering the method alone, without modification to the channel or junction geometries. The invention is applicable to both electroosmotic and electrophoretic transport, to combined electrokinetic transport, and to some special cases in which bulk fluid transport is driven by pressure gradients. It is further applicable to channels that are open, filled with a gel or filled with a porous or granular material.

  6. Impacts of sampling design and estimation methods on nutrient leaching of intensively monitored forest plots in the Netherlands.

    PubMed

    de Vries, W; Wieggers, H J J; Brus, D J

    2010-08-05

    Element fluxes through forest ecosystems are generally based on measurements of concentrations in soil solution at regular time intervals at plot locations sampled in a regular grid. Here we present spatially averaged annual element leaching fluxes in three Dutch forest monitoring plots using a new sampling strategy in which both sampling locations and sampling times are selected by probability sampling. Locations were selected by stratified random sampling with compact geographical blocks of equal surface area as strata. In each sampling round, six composite soil solution samples were collected, consisting of five aliquots, one per stratum. The plot-mean concentration was estimated by linear regression, so that the bias due to one or more strata being not represented in the composite samples is eliminated. The sampling times were selected in such a way that the cumulative precipitation surplus of the time interval between two consecutive sampling times was constant, using an estimated precipitation surplus averaged over the past 30 years. The spatially averaged annual leaching flux was estimated by using the modeled daily water flux as an ancillary variable. An important advantage of the new method is that the uncertainty in the estimated annual leaching fluxes due to spatial and temporal variation and resulting sampling errors can be quantified. Results of this new method were compared with the reference approach in which daily leaching fluxes were calculated by multiplying daily interpolated element concentrations with daily water fluxes and then aggregated to a year. Results show that the annual fluxes calculated with the reference method for the period 2003-2005, including all plots, elements and depths, lies only in 53% of the cases within the range of the average +/-2 times the standard error of the new method. Despite the differences in results, both methods indicate comparable N retention and strong Al mobilization in all plots, with Al leaching being

  7. A self-sampling method to obtain large volumes of undiluted cervicovaginal secretions.

    PubMed

    Boskey, Elizabeth R; Moench, Thomas R; Hees, Paul S; Cone, Richard A

    2003-02-01

    Studies of vaginal physiology and pathophysiology sometime require larger volumes of undiluted cervicovaginal secretions than can be obtained by current methods. A convenient method for self-sampling these secretions outside a clinical setting can facilitate such studies of reproductive health. The goal was to develop a vaginal self-sampling method for collecting large volumes of undiluted cervicovaginal secretions. A menstrual collection device (the Instead cup) was inserted briefly into the vagina to collect secretions that were then retrieved from the cup by centrifugation in a 50-ml conical tube. All 16 women asked to perform this procedure found it feasible and acceptable. Among 27 samples, an average of 0.5 g of secretions (range, 0.1-1.5 g) was collected. This is a rapid and convenient self-sampling method for obtaining relatively large volumes of undiluted cervicovaginal secretions. It should prove suitable for a wide range of assays, including those involving sexually transmitted diseases, microbicides, vaginal physiology, immunology, and pathophysiology.

  8. PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology

    USGS Publications Warehouse

    Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; DeSantis, Todd Z.; Zawada, David G.; Andersen, Gary L.

    2012-01-01

    Interest in coral microbial ecology has been increasing steadily over the last decade, yet standardized methods of sample collection still have not been defined. Two methods were compared for their ability to sample coral-associated microbial communities: tissue punches and foam swabs, the latter being less invasive and preferred by reef managers. Four colonies of star coral, Montastraea annularis, were sampled in the Dry Tortugas National Park (two healthy and two with white plague disease). The PhyloChip™ G3 microarray was used to assess microbial community structure of amplified 16S rRNA gene sequences. Samples clustered based on methodology rather than coral colony. Punch samples from healthy and diseased corals were distinct. All swab samples clustered closely together with the seawater control and did not group according to the health state of the corals. Although more microbial taxa were detected by the swab method, there is a much larger overlap between the water control and swab samples than punch samples, suggesting some of the additional diversity is due to contamination from water absorbed by the swab. While swabs are useful for noninvasive studies of the coral surface mucus layer, these results show that they are not optimal for studies of coral disease.

  9. PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology.

    PubMed

    Kellogg, Christina A; Piceno, Yvette M; Tom, Lauren M; DeSantis, Todd Z; Zawada, David G; Andersen, Gary L

    2012-01-01

    Interest in coral microbial ecology has been increasing steadily over the last decade, yet standardized methods of sample collection still have not been defined. Two methods were compared for their ability to sample coral-associated microbial communities: tissue punches and foam swabs, the latter being less invasive and preferred by reef managers. Four colonies of star coral, Montastraea annularis, were sampled in the Dry Tortugas National Park (two healthy and two with white plague disease). The PhyloChip™ G3 microarray was used to assess microbial community structure of amplified 16S rRNA gene sequences. Samples clustered based on methodology rather than coral colony. Punch samples from healthy and diseased corals were distinct. All swab samples clustered closely together with the seawater control and did not group according to the health state of the corals. Although more microbial taxa were detected by the swab method, there is a much larger overlap between the water control and swab samples than punch samples, suggesting some of the additional diversity is due to contamination from water absorbed by the swab. While swabs are useful for noninvasive studies of the coral surface mucus layer, these results show that they are not optimal for studies of coral disease. Published by Elsevier B.V.

  10. The importance of sound methodology in environmental DNA sampling

    Treesearch

    T. M. Wilcox; K. J. Carim; M. K. Young; K. S. McKelvey; T. W. Franklin; M. K. Schwartz

    2018-01-01

    Environmental DNA (eDNA) sampling - which enables inferences of species’ presence from genetic material in the environment - is a powerful tool for sampling rare fishes. Numerous studies have demonstrated that eDNA sampling generally provides greater probabilities of detection than traditional techniques (e.g., Thomsen et al. 2012; McKelvey et al. 2016; Valentini et al...

  11. 40 CFR 80.583 - What alternative sampling and testing requirements apply to importers who transport motor vehicle...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... applicable. (b) Quality assurance program. The importer must conduct a quality assurance program, as specified in this paragraph (b), for each truck or rail car loading terminal. (1) Quality assurance samples... an independent laboratory, and the terminal operator must not know in advance when samples are to be...

  12. Method and apparatus for processing a test sample to concentrate an analyte in the sample from a solvent in the sample

    DOEpatents

    Turner, Terry D.; Beller, Laurence S.; Clark, Michael L.; Klingler, Kerry M.

    1997-01-01

    A method of processing a test sample to concentrate an analyte in the sample from a solvent in the sample includes: a) boiling the test sample containing the analyte and solvent in a boiling chamber to a temperature greater than or equal to the solvent boiling temperature and less than the analyte boiling temperature to form a rising sample vapor mixture; b) passing the sample vapor mixture from the boiling chamber to an elongated primary separation tube, the separation tube having internal sidewalls and a longitudinal axis, the longitudinal axis being angled between vertical and horizontal and thus having an upper region and a lower region; c) collecting the physically transported liquid analyte on the internal sidewalls of the separation tube; and d) flowing the collected analyte along the angled internal sidewalls of the separation tube to and pass the separation tube lower region. The invention also includes passing a turbulence inducing wave through a vapor mixture to separate physically transported liquid second material from vaporized first material. Apparatus are also disclosed for effecting separations. Further disclosed is a fluidically powered liquid test sample withdrawal apparatus for withdrawing a liquid test sample from a test sample container and for cleaning the test sample container.

  13. Method and apparatus for processing a test sample to concentrate an analyte in the sample from a solvent in the sample

    DOEpatents

    Turner, T.D.; Beller, L.S.; Clark, M.L.; Klingler, K.M.

    1997-10-14

    A method of processing a test sample to concentrate an analyte in the sample from a solvent in the sample includes: (a) boiling the test sample containing the analyte and solvent in a boiling chamber to a temperature greater than or equal to the solvent boiling temperature and less than the analyte boiling temperature to form a rising sample vapor mixture; (b) passing the sample vapor mixture from the boiling chamber to an elongated primary separation tube, the separation tube having internal sidewalls and a longitudinal axis, the longitudinal axis being angled between vertical and horizontal and thus having an upper region and a lower region; (c) collecting the physically transported liquid analyte on the internal sidewalls of the separation tube; and (d) flowing the collected analyte along the angled internal sidewalls of the separation tube to and pass the separation tube lower region. The invention also includes passing a turbulence inducing wave through a vapor mixture to separate physically transported liquid second material from vaporized first material. Apparatus is also disclosed for effecting separations. Further disclosed is a fluidically powered liquid test sample withdrawal apparatus for withdrawing a liquid test sample from a test sample container and for cleaning the test sample container. 8 figs.

  14. Recording 2-D Nutation NQR Spectra by Random Sampling Method

    PubMed Central

    Sinyavsky, Nikolaj; Jadzyn, Maciej; Ostafin, Michal; Nogaj, Boleslaw

    2010-01-01

    The method of random sampling was introduced for the first time in the nutation nuclear quadrupole resonance (NQR) spectroscopy where the nutation spectra show characteristic singularities in the form of shoulders. The analytic formulae for complex two-dimensional (2-D) nutation NQR spectra (I = 3/2) were obtained and the condition for resolving the spectral singularities for small values of an asymmetry parameter η was determined. Our results show that the method of random sampling of a nutation interferogram allows significant reduction of time required to perform a 2-D nutation experiment and does not worsen the spectral resolution. PMID:20949121

  15. Quantifying Uncertainties from Presence Data Sampling Methods for Species Distribution Modeling: Focused on Vegetation.

    NASA Astrophysics Data System (ADS)

    Sung, S.; Kim, H. G.; Lee, D. K.; Park, J. H.; Mo, Y.; Kil, S.; Park, C.

    2016-12-01

    The impact of climate change has been observed throughout the globe. The ecosystem experiences rapid changes such as vegetation shift, species extinction. In these context, Species Distribution Model (SDM) is one of the popular method to project impact of climate change on the ecosystem. SDM basically based on the niche of certain species with means to run SDM present point data is essential to find biological niche of species. To run SDM for plants, there are certain considerations on the characteristics of vegetation. Normally, to make vegetation data in large area, remote sensing techniques are used. In other words, the exact point of presence data has high uncertainties as we select presence data set from polygons and raster dataset. Thus, sampling methods for modeling vegetation presence data should be carefully selected. In this study, we used three different sampling methods for selection of presence data of vegetation: Random sampling, Stratified sampling and Site index based sampling. We used one of the R package BIOMOD2 to access uncertainty from modeling. At the same time, we included BioCLIM variables and other environmental variables as input data. As a result of this study, despite of differences among the 10 SDMs, the sampling methods showed differences in ROC values, random sampling methods showed the lowest ROC value while site index based sampling methods showed the highest ROC value. As a result of this study the uncertainties from presence data sampling methods and SDM can be quantified.

  16. A distance limited method for sampling downed coarse woody debris

    Treesearch

    Jeffrey H. Gove; Mark J. Ducey; Harry T. Valentine; Michael S. Williams

    2012-01-01

    A new sampling method for down coarse woody debris is proposed based on limiting the perpendicular distance from individual pieces to a randomly chosen sample point. Two approaches are presented that allow different protocols to be used to determine field measurements; estimators for each protocol are also developed. Both protocols are compared via simulation against...

  17. Adaptive cluster sampling: An efficient method for assessing inconspicuous species

    Treesearch

    Andrea M. Silletti; Joan Walker

    2003-01-01

    Restorationistis typically evaluate the success of a project by estimating the population sizes of species that have been planted or seeded. Because total census is raely feasible, they must rely on sampling methods for population estimates. However, traditional random sampling designs may be inefficient for species that, for one reason or another, are challenging to...

  18. Comparative evaluation of four mosquitoes sampling methods in rice irrigation schemes of lower Moshi, northern Tanzania.

    PubMed

    Kweka, Eliningaya J; Mahande, Aneth M

    2009-07-06

    Adult malaria vector sampling is the most important parameter for setting up an intervention and understanding disease dynamics in malaria endemic areas. The intervention will ideally be species-specific according to sampling output. It was the objective of this study to evaluate four sampling techniques, namely human landing catch, pit shelter, indoor resting collection and odour-baited entry trap. These four sampling methods were evaluated simultaneously for thirty days during October 2008, a season of low mosquitoes density and malaria transmission. These trapping methods were performed in one village for maximizing homogeneity in mosquito density. The cattle and man used in odour-baited entry trap were rotated between the chambers to avoid bias. A total of 3,074 mosquitoes were collected. Among these 1,780 (57.9%) were Anopheles arabiensis and 1,294 (42.1%) were Culex quinquefasciatus. Each trap sampled different number of mosquitoes, Indoor resting collection collected 335 (10.9%), Odour-baited entry trap-cow 1,404 (45.7%), Odour-baited entry trap-human 378 (12.3%), Pit shelter 562 (18.3%) and HLC 395 (12.8%). General linear model univariate analysis method was used, position of the trapping method had no effect on mosquito density catch (DF = 4, F = 35.596, P = 0.78). Days variation had no effect on the collected density too (DF = 29, F = 4.789, P = 0.09). The sampling techniques had significant impact on the caught mosquito densities (DF = 4, F = 34.636, P < 0.0001). The Wilcoxon pair-wise comparison between mosquitoes collected in human landing catch and pit shelter was significant (Z = -3.849, P < 0.0001), human landing catch versus Indoor resting collection was not significant (Z = -0.502, P = 0.615), human landing catch versus odour-baited entry trap-man was significant (Z = -2.687, P = 0.007), human landing catch versus odour-baited entry trap-cow was significant (Z = -3.127, P = 0.002). Odour-baited traps with different baits and pit shelter have shown

  19. A novel heterogeneous training sample selection method on space-time adaptive processing

    NASA Astrophysics Data System (ADS)

    Wang, Qiang; Zhang, Yongshun; Guo, Yiduo

    2018-04-01

    The performance of ground target detection about space-time adaptive processing (STAP) decreases when non-homogeneity of clutter power is caused because of training samples contaminated by target-like signals. In order to solve this problem, a novel nonhomogeneous training sample selection method based on sample similarity is proposed, which converts the training sample selection into a convex optimization problem. Firstly, the existing deficiencies on the sample selection using generalized inner product (GIP) are analyzed. Secondly, the similarities of different training samples are obtained by calculating mean-hausdorff distance so as to reject the contaminated training samples. Thirdly, cell under test (CUT) and the residual training samples are projected into the orthogonal subspace of the target in the CUT, and mean-hausdorff distances between the projected CUT and training samples are calculated. Fourthly, the distances are sorted in order of value and the training samples which have the bigger value are selective preference to realize the reduced-dimension. Finally, simulation results with Mountain-Top data verify the effectiveness of the proposed method.

  20. Sampling and data handling methods for inhalable particulate sampling. Final report nov 78-dec 80

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Smith, W.B.; Cushing, K.M.; Johnson, J.W.

    1982-05-01

    The report reviews the objectives of a research program on sampling and measuring particles in the inhalable particulate (IP) size range in emissions from stationary sources, and describes methods and equipment required. A computer technique was developed to analyze data on particle-size distributions of samples taken with cascade impactors from industrial process streams. Research in sampling systems for IP matter included concepts for maintaining isokinetic sampling conditions, necessary for representative sampling of the larger particles, while flowrates in the particle-sizing device were constant. Laboratory studies were conducted to develop suitable IP sampling systems with overall cut diameters of 15 micrometersmore » and conforming to a specified collection efficiency curve. Collection efficiencies were similarly measured for a horizontal elutriator. Design parameters were calculated for horizontal elutriators to be used with impactors, the EPA SASS train, and the EPA FAS train. Two cyclone systems were designed and evaluated. Tests on an Andersen Size Selective Inlet, a 15-micrometer precollector for high-volume samplers, showed its performance to be with the proposed limits for IP samplers. A stack sampling system was designed in which the aerosol is diluted in flow patterns and with mixing times simulating those in stack plumes.« less

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

    PubMed

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

    2014-01-01

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

  2. Effectiveness of sampling methods employed for Acanthamoeba keratitis diagnosis by culture.

    PubMed

    Muiño, Laura; Rodrigo, Donoso; Villegas, Rodrigo; Romero, Pablo; Peredo, Daniel E; Vargas, Rafael A; Liempi, Daniela; Osuna, Antonio; Jercic, María Isabel

    2018-06-18

    This retrospective, observational study was designed to evaluate the effectiveness of the sampling methods commonly used for the collection of corneal scrapes for the diagnosis of Acanthamoeba keratitis (AK) by culture, in terms of their ability to provide a positive result. A total of 553 samples from 380 patients with suspected AK received at the Parasitology Section of the Public Health Institute of Chile, between January 2005 and December 2015, were evaluated. A logistic regression model was used to determine the correlation between the culture outcome (positive or negative) and the method for sample collection. The year of sample collection was also included in the analysis as a confounding variable. Three hundred and sixty-five samples (27%) from 122 patients (32.1%) were positive by culture. The distribution of sample types was as follows: 142 corneal scrapes collected using a modified bezel needle (a novel method developed by a team of Chilean corneologists), 176 corneal scrapes obtained using a scalpel, 50 corneal biopsies, 30 corneal swabs, and 155 non-biological materials including contact lens and its paraphernalia. Biopsy provided the highest likelihood ratio for a positive result by culture (1.89), followed by non-biological materials (1.10) and corneal scrapes obtained using a modified needle (1.00). The lowest likelihood ratio was estimated for corneal scrapes obtained using a scalpel (0.88) and cotton swabs (0.78). Apart from biopsy, optimum corneal samples for the improved diagnosis of AK can be obtained using a modified bezel needle instead of a scalpel, while cotton swabs are not recommended.

  3. Sampling for Patient Exit Interviews: Assessment of Methods Using Mathematical Derivation and Computer Simulations.

    PubMed

    Geldsetzer, Pascal; Fink, Günther; Vaikath, Maria; Bärnighausen, Till

    2018-02-01

    (1) To evaluate the operational efficiency of various sampling methods for patient exit interviews; (2) to discuss under what circumstances each method yields an unbiased sample; and (3) to propose a new, operationally efficient, and unbiased sampling method. Literature review, mathematical derivation, and Monte Carlo simulations. Our simulations show that in patient exit interviews it is most operationally efficient if the interviewer, after completing an interview, selects the next patient exiting the clinical consultation. We demonstrate mathematically that this method yields a biased sample: patients who spend a longer time with the clinician are overrepresented. This bias can be removed by selecting the next patient who enters, rather than exits, the consultation room. We show that this sampling method is operationally more efficient than alternative methods (systematic and simple random sampling) in most primary health care settings. Under the assumption that the order in which patients enter the consultation room is unrelated to the length of time spent with the clinician and the interviewer, selecting the next patient entering the consultation room tends to be the operationally most efficient unbiased sampling method for patient exit interviews. © 2016 The Authors. Health Services Research published by Wiley Periodicals, Inc. on behalf of Health Research and Educational Trust.

  4. Sampling Methods for Detection and Monitoring of the Asian Citrus Psyllid (Hemiptera: Psyllidae).

    PubMed

    Monzo, C; Arevalo, H A; Jones, M M; Vanaclocha, P; Croxton, S D; Qureshi, J A; Stansly, P A

    2015-06-01

    The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama is a key pest of citrus due to its role as vector of citrus greening disease or "huanglongbing." ACP monitoring is considered an indispensable tool for management of vector and disease. In the present study, datasets collected between 2009 and 2013 from 245 citrus blocks were used to evaluate precision, sensitivity for detection, and efficiency of five sampling methods. The number of samples needed to reach a 0.25 standard error-mean ratio was estimated using Taylor's power law and used to compare precision among sampling methods. Comparison of detection sensitivity and time expenditure (cost) between stem-tap and other sampling methodologies conducted consecutively at the same location were also assessed. Stem-tap sampling was the most efficient sampling method when ACP densities were moderate to high and served as the basis for comparison with all other methods. Protocols that grouped trees near randomly selected locations across the block were more efficient than sampling trees at random across the block. Sweep net sampling was similar to stem-taps in number of captures per sampled unit, but less precise at any ACP density. Yellow sticky traps were 14 times more sensitive than stem-taps but much more time consuming and thus less efficient except at very low population densities. Visual sampling was efficient for detecting and monitoring ACP at low densities. Suction sampling was time consuming and taxing but the most sensitive of all methods for detection of sparse populations. This information can be used to optimize ACP monitoring efforts. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  5. Methods for collection and analysis of aquatic biological and microbiological samples

    USGS Publications Warehouse

    Britton, L.J.; Greeson, P.E.

    1989-01-01

    The series of chapters on techniques describes methods used by the U.S. Geological Survey for planning and conducting water-resources investigations. The material is arranged under major subject headings called books and is further subdivided into sections and chapters. Book 5 is on laboratory analysis. Section A is on water. The unit of publication, the chapter, is limited to a narrow field of subject matter. "Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" is the fourth chapter to be published under Section A of Book 5. The chapter number includes the letter of the section.This chapter was prepared by several aquatic biologists and microbiologists of the U.S. Geological Survey to provide accurate and precise methods for the collection and analysis of aquatic biological and microbiological samples.Use of brand, firm, and trade names in this chapter is for identification purposes only and does not constitute endorsement by the U.S. Geological Survey.This chapter supersedes "Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" edited by P.E. Greeson, T.A. Ehlke, G.A. Irwin, B.W. Lium, and K.V. Slack (U.S. Geological Survey Techniques of Water-Resources Investigations, Book 5, Chapter A4, 1977) and also supersedes "A Supplement to-Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" by P.E. Greeson (U.S. Geological Survey Techniques of Water-Resources Investigations, Book 5, Chapter A4), Open-File Report 79-1279, 1979.

  6. Optical Methods for Identifying Hard Clay Core Samples During Petrophysical Studies

    NASA Astrophysics Data System (ADS)

    Morev, A. V.; Solovyeva, A. V.; Morev, V. A.

    2018-01-01

    X-ray phase analysis of the general mineralogical composition of core samples from one of the West Siberian fields was performed. Electronic absorption spectra of the clay core samples with an added indicator were studied. The speed and availability of applying the two methods in petrophysical laboratories during sample preparation for standard and special studies were estimated.

  7. Burnout and Engagement: Relative Importance of Predictors and Outcomes in Two Health Care Worker Samples.

    PubMed

    Fragoso, Zachary L; Holcombe, Kyla J; McCluney, Courtney L; Fisher, Gwenith G; McGonagle, Alyssa K; Friebe, Susan J

    2016-06-09

    This study's purpose was twofold: first, to examine the relative importance of job demands and resources as predictors of burnout and engagement, and second, the relative importance of engagement and burnout related to health, depressive symptoms, work ability, organizational commitment, and turnover intentions in two samples of health care workers. Nurse leaders (n = 162) and licensed emergency medical technicians (EMTs; n = 102) completed surveys. In both samples, job demands predicted burnout more strongly than job resources, and job resources predicted engagement more strongly than job demands. Engagement held more weight than burnout for predicting commitment, and burnout held more weight for predicting health outcomes, depressive symptoms, and work ability. Results have implications for the design, evaluation, and effectiveness of workplace interventions to reduce burnout and improve engagement among health care workers. Actionable recommendations for increasing engagement and decreasing burnout in health care organizations are provided. © 2016 The Author(s).

  8. Determining an Appropriate Sampling Method. School Accountability Series. Monograph 3.

    ERIC Educational Resources Information Center

    McCallon, Earl; McClaran, Rutledge

    This is one of a series of eight short monographs intended to aid practicing educators in planning and conducting accountability programs in schools. This booklet discusses how to determine a sampling method that is appropriate to the objectives of a particular research or evaluation effort. Short sections focus in turn on why and when to sample,…

  9. Evaluation of sampling methods for measuring exposure to volatile inorganic acids in workplace air. Part 1: sampling hydrochloric acid (HCl) and nitric acid (HNO₃) from a test gas atmosphere.

    PubMed

    Howe, Alan; Musgrove, Darren; Breuer, Dietmar; Gusbeth, Krista; Moritz, Andreas; Demange, Martine; Oury, Véronique; Rousset, Davy; Dorotte, Michel

    2011-08-01

    Historically, workplace exposure to the volatile inorganic acids hydrochloric acid (HCl) and nitric acid (HNO(3)) has been determined mostly by collection on silica gel sorbent tubes and analysis of the corresponding anions by ion chromatography (IC). However, HCl and HNO(3) can be present in workplace air in the form of mist as well as vapor, so it is important to sample the inhalable fraction of airborne particles. As sorbent tubes exhibit a low sampling efficiency for inhalable particles, a more suitable method was required. This is the first of two articles on "Evaluation of Sampling Methods for Measuring Exposure to Volatile Inorganic Acids in Workplace Air" and describes collaborative sampling exercises carried out to evaluate an alternative method for sampling HCl and HNO(3) using sodium carbonate-impregnated filters. The second article describes sampling capacity and breakthrough tests. The method was found to perform well and a quartz fiber filter impregnated with 500 μL of 1 M Na(2)CO(3) (10% (m/v) Na(2)CO(3)) was found to have sufficient sampling capacity for use in workplace air measurement. A pre-filter is required to remove particulate chlorides and nitrates that when present would otherwise result in a positive interference. A GSP sampler fitted with a plastic cone, a closed face cassette, or a plastic IOM sampler were all found to be suitable for mounting the pre-filter and sampling filter(s), but care has to be taken with the IOM sampler to ensure that the sampler is tightly closed to avoid leaks. HCl and HNO(3) can react with co-sampled particulate matter on the pre-filter, e.g., zinc oxide, leading to low results, and stronger acids can react with particulate chlorides and nitrates removed by the pre-filter to liberate HCl and HNO(3), which are subsequently collected on the sampling filter, leading to high results. However, although there is this potential for both positive and negative interferences in the measurement, these are unavoidable

  10. Geostatistical Sampling Methods for Efficient Uncertainty Analysis in Flow and Transport Problems

    NASA Astrophysics Data System (ADS)

    Liodakis, Stylianos; Kyriakidis, Phaedon; Gaganis, Petros

    2015-04-01

    In hydrogeological applications involving flow and transport of in heterogeneous porous media the spatial distribution of hydraulic conductivity is often parameterized in terms of a lognormal random field based on a histogram and variogram model inferred from data and/or synthesized from relevant knowledge. Realizations of simulated conductivity fields are then generated using geostatistical simulation involving simple random (SR) sampling and are subsequently used as inputs to physically-based simulators of flow and transport in a Monte Carlo framework for evaluating the uncertainty in the spatial distribution of solute concentration due to the uncertainty in the spatial distribution of hydraulic con- ductivity [1]. Realistic uncertainty analysis, however, calls for a large number of simulated concentration fields; hence, can become expensive in terms of both time and computer re- sources. A more efficient alternative to SR sampling is Latin hypercube (LH) sampling, a special case of stratified random sampling, which yields a more representative distribution of simulated attribute values with fewer realizations [2]. Here, term representative implies realizations spanning efficiently the range of possible conductivity values corresponding to the lognormal random field. In this work we investigate the efficiency of alternative methods to classical LH sampling within the context of simulation of flow and transport in a heterogeneous porous medium. More precisely, we consider the stratified likelihood (SL) sampling method of [3], in which attribute realizations are generated using the polar simulation method by exploring the geometrical properties of the multivariate Gaussian distribution function. In addition, we propose a more efficient version of the above method, here termed minimum energy (ME) sampling, whereby a set of N representative conductivity realizations at M locations is constructed by: (i) generating a representative set of N points distributed on the

  11. Comparison of depth-specific groundwater sampling methods and their influence on hydrochemistry, isotopy and dissolved gases - Experiences from the Fuhrberger Feld, Germany

    NASA Astrophysics Data System (ADS)

    Houben, Georg J.; Koeniger, Paul; Schloemer, Stefan; Gröger-Trampe, Jens; Sültenfuß, Jürgen

    2018-02-01

    Depth-specific sampling of groundwater is important for a variety of hydrogeological applications. Several sampling methods are available but comparably little is known about how their results compare. Therefore, samples from regular observation wells (short screen), micro-filters and direct push were compared for two sites with differing hydrogeological conditions and land use, both located in the Fuhrberger Feld, Germany. The encountered hydrochemical zonation requires a high resolution of 1 m or better, which the available small number of regular observation wells could only roughly mirror. Because the three methods employ significantly varying pumping rates and therefore, have varying spatial origins of the sample, individual concentrations at similar depths may differ significantly. In a hydrologically and chemically dynamical environment such as the agricultural site, this effect becomes more pronounced than for the more stable forest site. The micro-filters are probably the most depth-specific, but showed distinctly lower concentrations for dissolved gases than the other two methods, due to degassing during sampling. They should thus not be used for any method that relies on dissolved gas analysis.

  12. A comparison of four sampling methods among men having sex with men in China: implications for HIV/STD surveillance and prevention

    PubMed Central

    Guo, Yan; Li, Xiaoming; Fang, Xiaoyi; Lin, Xiuyun; Song, Yan; Jiang, Shuling; Stanton, Bonita

    2011-01-01

    Sample representativeness remains one of the challenges in effective HIV/STD surveillance and prevention targeting MSM worldwide. Although convenience samples are widely used in studies of MSM, previous studies suggested that these samples might not be representative of the broader MSM population. This issue becomes even more critical in many developing countries where needed resources for conducting probability sampling are limited. We examined variations in HIV and Syphilis infections and sociodemographic and behavioral factors among 307 young migrant MSM recruited using four different convenience sampling methods (peer outreach, informal social network, Internet, and venue-based) in Beijing, China in 2009. The participants completed a self-administered survey and provided blood specimens for HIV/STD testing. Among the four MSM samples using different recruitment methods, rates of HIV infections were 5.1%, 5.8%, 7.8%, and 3.4%; rates of Syphilis infection were 21.8%, 36.2%, 11.8%, and 13.8%; rates of inconsistent condom use were 57%, 52%, 58%, and 38%. Significant differences were found in various sociodemographic characteristics (e.g., age, migration history, education, income, places of employment) and risk behaviors (e.g., age at first sex, number of sex partners, involvement in commercial sex, and substance use) among samples recruited by different sampling methods. The results confirmed the challenges of obtaining representative MSM samples and underscored the importance of using multiple sampling methods to reach MSM from diverse backgrounds and in different social segments and to improve the representativeness of the MSM samples when the use of probability sampling approach is not feasible. PMID:21711162

  13. Fluid sampling apparatus and method

    DOEpatents

    Yeamans, David R.

    1998-01-01

    Incorporation of a bellows in a sampling syringe eliminates ingress of contaminants, permits replication of amounts and compression of multiple sample injections, and enables remote sampling for off-site analysis.

  14. Public views on the donation and use of human biological samples in biomedical research: a mixed methods study

    PubMed Central

    Lewis, Celine; Clotworthy, Margaret; Hilton, Shona; Magee, Caroline; Robertson, Mark J; Stubbins, Lesley J; Corfield, Julie

    2013-01-01

    Objective A mixed methods study exploring the UK general public's willingness to donate human biosamples (HBSs) for biomedical research. Setting Cross-sectional focus groups followed by an online survey. Participants Twelve focus groups (81 participants) selectively sampled to reflect a range of demographic groups; 1110 survey responders recruited through a stratified sampling method with quotas set on sex, age, geographical location, socioeconomic group and ethnicity. Main outcome measures (1) Identify participants’ willingness to donate HBSs for biomedical research, (2) explore acceptability towards donating different types of HBSs in various settings and (3) explore preferences regarding use and access to HBSs. Results 87% of survey participants thought donation of HBSs was important and 75% wanted to be asked to donate in general. Responders who self-reported having some or good knowledge of the medical research process were significantly more likely to want to donate (p<0.001). Reasons why focus group participants saw donation as important included: it was a good way of reciprocating for the medical treatment received; it was an important way of developing drugs and treatments; residual tissue would otherwise go to waste and they or their family members might benefit. The most controversial types of HBSs to donate included: brain post mortem (29% would donate), eyes post mortem (35%), embryos (44%), spare eggs (48%) and sperm (58%). Regarding the use of samples, there were concerns over animal research (34%), research conducted outside the UK (35%), and research conducted by pharmaceutical companies (56%), although education and discussion were found to alleviate such concerns. Conclusions There is a high level of public support and willingness to donate HBSs for biomedical research. Underlying concerns exist regarding the use of certain types of HBSs and conditions under which they are used. Improved education and more controlled forms of consent for

  15. 40 CFR 80.8 - Sampling methods for gasoline, diesel fuel, fuel additives, and renewable fuels.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 17 2014-07-01 2014-07-01 false Sampling methods for gasoline, diesel... Provisions § 80.8 Sampling methods for gasoline, diesel fuel, fuel additives, and renewable fuels. The sampling methods specified in this section shall be used to collect samples of gasoline, diesel fuel...

  16. Systems and methods for separating particles and/or substances from a sample fluid

    DOEpatents

    Mariella, Jr., Raymond P.; Dougherty, George M.; Dzenitis, John M.; Miles, Robin R.; Clague, David S.

    2016-11-01

    Systems and methods for separating particles and/or toxins from a sample fluid. A method according to one embodiment comprises simultaneously passing a sample fluid and a buffer fluid through a chamber such that a fluidic interface is formed between the sample fluid and the buffer fluid as the fluids pass through the chamber, the sample fluid having particles of interest therein; applying a force to the fluids for urging the particles of interest to pass through the interface into the buffer fluid; and substantially separating the buffer fluid from the sample fluid.

  17. A comparison of four porewater sampling methods for metal mixtures and dissolved organic carbon and the implications for sediment toxicity evaluations

    USGS Publications Warehouse

    Cleveland, Danielle; Brumbaugh, William G.; MacDonald, Donald D.

    2017-01-01

    Evaluations of sediment quality conditions are commonly conducted using whole-sediment chemistry analyses but can be enhanced by evaluating multiple lines of evidence, including measures of the bioavailable forms of contaminants. In particular, porewater chemistry data provide information that is directly relevant for interpreting sediment toxicity data. Various methods for sampling porewater for trace metals and dissolved organic carbon (DOC), which is an important moderator of metal bioavailability, have been employed. The present study compares the peeper, push point, centrifugation, and diffusive gradients in thin films (DGT) methods for the quantification of 6 metals and DOC. The methods were evaluated at low and high concentrations of metals in 3 sediments having different concentrations of total organic carbon and acid volatile sulfide and different particle-size distributions. At low metal concentrations, centrifugation and push point sampling resulted in up to 100 times higher concentrations of metals and DOC in porewater compared with peepers and DGTs. At elevated metal levels, the measured concentrations were in better agreement among the 4 sampling techniques. The results indicate that there can be marked differences among operationally different porewater sampling methods, and it is unclear if there is a definitive best method for sampling metals and DOC in porewater.

  18. A fast learning method for large scale and multi-class samples of SVM

    NASA Astrophysics Data System (ADS)

    Fan, Yu; Guo, Huiming

    2017-06-01

    A multi-class classification SVM(Support Vector Machine) fast learning method based on binary tree is presented to solve its low learning efficiency when SVM processing large scale multi-class samples. This paper adopts bottom-up method to set up binary tree hierarchy structure, according to achieved hierarchy structure, sub-classifier learns from corresponding samples of each node. During the learning, several class clusters are generated after the first clustering of the training samples. Firstly, central points are extracted from those class clusters which just have one type of samples. For those which have two types of samples, cluster numbers of their positive and negative samples are set respectively according to their mixture degree, secondary clustering undertaken afterwards, after which, central points are extracted from achieved sub-class clusters. By learning from the reduced samples formed by the integration of extracted central points above, sub-classifiers are obtained. Simulation experiment shows that, this fast learning method, which is based on multi-level clustering, can guarantee higher classification accuracy, greatly reduce sample numbers and effectively improve learning efficiency.

  19. Fluid sampling apparatus and method

    DOEpatents

    Yeamans, D.R.

    1998-02-03

    Incorporation of a bellows in a sampling syringe eliminates ingress of contaminants, permits replication of amounts and compression of multiple sample injections, and enables remote sampling for off-site analysis. 3 figs.

  20. ADAPTIVE ANNEALED IMPORTANCE SAMPLING FOR MULTIMODAL POSTERIOR EXPLORATION AND MODEL SELECTION WITH APPLICATION TO EXTRASOLAR PLANET DETECTION

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Liu, Bin, E-mail: bins@ieee.org

    2014-07-01

    We describe an algorithm that can adaptively provide mixture summaries of multimodal posterior distributions. The parameter space of the involved posteriors ranges in size from a few dimensions to dozens of dimensions. This work was motivated by an astrophysical problem called extrasolar planet (exoplanet) detection, wherein the computation of stochastic integrals that are required for Bayesian model comparison is challenging. The difficulty comes from the highly nonlinear models that lead to multimodal posterior distributions. We resort to importance sampling (IS) to estimate the integrals, and thus translate the problem to be how to find a parametric approximation of the posterior.more » To capture the multimodal structure in the posterior, we initialize a mixture proposal distribution and then tailor its parameters elaborately to make it resemble the posterior to the greatest extent possible. We use the effective sample size (ESS) calculated based on the IS draws to measure the degree of approximation. The bigger the ESS is, the better the proposal resembles the posterior. A difficulty within this tailoring operation lies in the adjustment of the number of mixing components in the mixture proposal. Brute force methods just preset it as a large constant, which leads to an increase in the required computational resources. We provide an iterative delete/merge/add process, which works in tandem with an expectation-maximization step to tailor such a number online. The efficiency of our proposed method is tested via both simulation studies and real exoplanet data analysis.« less

  1. Twenty-four cases of imported zika virus infections diagnosed by molecular methods.

    PubMed

    Alejo-Cancho, Izaskun; Torner, Nuria; Oliveira, Inés; Martínez, Ana; Muñoz, José; Jane, Mireia; Gascón, Joaquim; Requena-Méndez, Ana; Vilella, Anna; Marcos, M Ángeles; Pinazo, María Jesús; Gonzalo, Verónica; Rodriguez, Natalia; Martínez, Miguel J

    2016-10-01

    Zika virus is an emerging flavivirus widely spreading through Latin America. Molecular diagnosis of the infection can be performed using serum, urine and saliva samples, although a well-defined diagnostic algorithm is not yet established. We describe a series of 24 cases of imported zika virus infection into Catalonia (northeastern Spain). Based on our findings, testing of paired serum and urine samples is recommended. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Effect of the absolute statistic on gene-sampling gene-set analysis methods.

    PubMed

    Nam, Dougu

    2017-06-01

    Gene-set enrichment analysis and its modified versions have commonly been used for identifying altered functions or pathways in disease from microarray data. In particular, the simple gene-sampling gene-set analysis methods have been heavily used for datasets with only a few sample replicates. The biggest problem with this approach is the highly inflated false-positive rate. In this paper, the effect of absolute gene statistic on gene-sampling gene-set analysis methods is systematically investigated. Thus far, the absolute gene statistic has merely been regarded as a supplementary method for capturing the bidirectional changes in each gene set. Here, it is shown that incorporating the absolute gene statistic in gene-sampling gene-set analysis substantially reduces the false-positive rate and improves the overall discriminatory ability. Its effect was investigated by power, false-positive rate, and receiver operating curve for a number of simulated and real datasets. The performances of gene-set analysis methods in one-tailed (genome-wide association study) and two-tailed (gene expression data) tests were also compared and discussed.

  3. Detection and monitoring of invasive exotic plants: a comparison of four sampling methods

    Treesearch

    Cynthia D. Huebner

    2007-01-01

    The ability to detect and monitor exotic invasive plants is likely to vary depending on the sampling method employed. Methods with strong qualitative thoroughness for species detection often lack the intensity necessary to monitor vegetation change. Four sampling methods (systematic plot, stratified-random plot, modified Whittaker, and timed meander) in hemlock and red...

  4. RESULTS FROM EPA FUNDED RESEARCH PROGRAMS ON THE IMPORTANCE OF PURGE VOLUME, SAMPLE VOLUME, SAMPLE FLOW RATE AND TEMPORAL VARIATIONS ON SOIL GAS CONCENTRATIONS

    EPA Science Inventory

    Two research studies funded and overseen by EPA have been conducted since October 2006 on soil gas sampling methods and variations in shallow soil gas concentrations with the purpose of improving our understanding of soil gas methods and data for vapor intrusion applications. Al...

  5. Suitability of the line intersect method for sampling hardwood logging residues

    Treesearch

    A. Jeff Martin

    1976-01-01

    The line intersect method of sampling logging residues was tested in Appalachian hardwoods and was found to provide unbiased estimates of the volume of residue in cubic feet per acre. Thirty-two chains of sample line were established on each of sixteen 1-acre plots on cutover areas in a variety of conditions. Estimates from these samples were then compared to actual...

  6. 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

  7. Methods for collection and analysis of aquatic biological and microbiological samples

    USGS Publications Warehouse

    Greeson, Phillip E.; Ehlke, T.A.; Irwin, G.A.; Lium, B.W.; Slack, K.V.

    1977-01-01

    Chapter A4 contains methods used by the U.S. Geological Survey to collect, preserve, and analyze waters to determine their biological and microbiological properties. Part 1 discusses biological sampling and sampling statistics. The statistical procedures are accompanied by examples. Part 2 consists of detailed descriptions of more than 45 individual methods, including those for bacteria, phytoplankton, zooplankton, seston, periphyton, macrophytes, benthic invertebrates, fish and other vertebrates, cellular contents, productivity, and bioassays. Each method is summarized, and the application, interferences, apparatus, reagents, collection, analysis, calculations, reporting of results, precision and references are given. Part 3 consists of a glossary. Part 4 is a list of taxonomic references.

  8. Fast identification of microplastics in complex environmental samples by a thermal degradation method.

    PubMed

    Dümichen, Erik; Eisentraut, Paul; Bannick, Claus Gerhard; Barthel, Anne-Kathrin; Senz, Rainer; Braun, Ulrike

    2017-05-01

    In order to determine the relevance of microplastic particles in various environmental media, comprehensive investigations are needed. However, no analytical method exists for fast identification and quantification. At present, optical spectroscopy methods like IR and RAMAN imaging are used. Due to their time consuming procedures and uncertain extrapolation, reliable monitoring is difficult. For analyzing polymers Py-GC-MS is a standard method. However, due to a limited sample amount of about 0.5 mg it is not suited for analysis of complex sample mixtures like environmental samples. Therefore, we developed a new thermoanalytical method as a first step for identifying microplastics in environmental samples. A sample amount of about 20 mg, which assures the homogeneity of the sample, is subjected to complete thermal decomposition. The specific degradation products of the respective polymer are adsorbed on a solid-phase adsorber and subsequently analyzed by thermal desorption gas chromatography mass spectrometry. For certain identification, the specific degradation products for the respective polymer were selected first. Afterwards real environmental samples from the aquatic (three different rivers) and the terrestrial (bio gas plant) systems were screened for microplastics. Mainly polypropylene (PP), polyethylene (PE) and polystyrene (PS) were identified for the samples from the bio gas plant and PE and PS from the rivers. However, this was only the first step and quantification measurements will follow. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Small Body GN and C Research Report: G-SAMPLE - An In-Flight Dynamical Method for Identifying Sample Mass [External Release Version

    NASA Technical Reports Server (NTRS)

    Carson, John M., III; Bayard, David S.

    2006-01-01

    G-SAMPLE is an in-flight dynamical method for use by sample collection missions to identify the presence and quantity of collected sample material. The G-SAMPLE method implements a maximum-likelihood estimator to identify the collected sample mass, based on onboard force sensor measurements, thruster firings, and a dynamics model of the spacecraft. With G-SAMPLE, sample mass identification becomes a computation rather than an extra hardware requirement; the added cost of cameras or other sensors for sample mass detection is avoided. Realistic simulation examples are provided for a spacecraft configuration with a sample collection device mounted on the end of an extended boom. In one representative example, a 1000 gram sample mass is estimated to within 110 grams (95% confidence) under realistic assumptions of thruster profile error, spacecraft parameter uncertainty, and sensor noise. For convenience to future mission design, an overall sample-mass estimation error budget is developed to approximate the effect of model uncertainty, sensor noise, data rate, and thrust profile error on the expected estimate of collected sample mass.

  10. Sampling methods, dispersion patterns, and fixed precision sequential sampling plans for western flower thrips (Thysanoptera: Thripidae) and cotton fleahoppers (Hemiptera: Miridae) in cotton.

    PubMed

    Parajulee, M N; Shrestha, R B; Leser, J F

    2006-04-01

    A 2-yr field study was conducted to examine the effectiveness of two sampling methods (visual and plant washing techniques) for western flower thrips, Frankliniella occidentalis (Pergande), and five sampling methods (visual, beat bucket, drop cloth, sweep net, and vacuum) for cotton fleahopper, Pseudatomoscelis seriatus (Reuter), in Texas cotton, Gossypium hirsutum (L.), and to develop sequential sampling plans for each pest. The plant washing technique gave similar results to the visual method in detecting adult thrips, but the washing technique detected significantly higher number of thrips larvae compared with the visual sampling. Visual sampling detected the highest number of fleahoppers followed by beat bucket, drop cloth, vacuum, and sweep net sampling, with no significant difference in catch efficiency between vacuum and sweep net methods. However, based on fixed precision cost reliability, the sweep net sampling was the most cost-effective method followed by vacuum, beat bucket, drop cloth, and visual sampling. Taylor's Power Law analysis revealed that the field dispersion patterns of both thrips and fleahoppers were aggregated throughout the crop growing season. For thrips management decision based on visual sampling (0.25 precision), 15 plants were estimated to be the minimum sample size when the estimated population density was one thrips per plant, whereas the minimum sample size was nine plants when thrips density approached 10 thrips per plant. The minimum visual sample size for cotton fleahoppers was 16 plants when the density was one fleahopper per plant, but the sample size decreased rapidly with an increase in fleahopper density, requiring only four plants to be sampled when the density was 10 fleahoppers per plant. Sequential sampling plans were developed and validated with independent data for both thrips and cotton fleahoppers.

  11. Optimization of fecal cytology in the dog: comparison of three sampling methods.

    PubMed

    Frezoulis, Petros S; Angelidou, Elisavet; Diakou, Anastasia; Rallis, Timoleon S; Mylonakis, Mathios E

    2017-09-01

    Dry-mount fecal cytology (FC) is a component of the diagnostic evaluation of gastrointestinal diseases. There is limited information on the possible effect of the sampling method on the cytologic findings of healthy dogs or dogs admitted with diarrhea. We aimed to: (1) establish sampling method-specific expected values of selected cytologic parameters (isolated or clustered epithelial cells, neutrophils, lymphocytes, macrophages, spore-forming rods) in clinically healthy dogs; (2) investigate if the detection of cytologic abnormalities differs among methods in dogs admitted with diarrhea; and (3) investigate if there is any association between FC abnormalities and the anatomic origin (small- or large-bowel diarrhea) or the chronicity of diarrhea. Sampling with digital examination (DE), rectal scraping (RS), and rectal lavage (RL) was prospectively assessed in 37 healthy and 34 diarrheic dogs. The median numbers of isolated ( p = 0.000) or clustered ( p = 0.002) epithelial cells, and of lymphocytes ( p = 0.000), differed among the 3 methods in healthy dogs. In the diarrheic dogs, the RL method was the least sensitive in detecting neutrophils, and isolated or clustered epithelial cells. Cytologic abnormalities were not associated with the origin or the chronicity of diarrhea. Sampling methods differed in their sensitivity to detect abnormalities in FC; DE or RS may be of higher sensitivity compared to RL. Anatomic origin or chronicity of diarrhea do not seem to affect the detection of cytologic abnormalities.

  12. Molecular Method for Detection of Total Coliforms in Drinking Water Samples

    PubMed Central

    Boudreau, Dominique K.; Bisson, Marc-Antoine; Dion-Dupont, Vanessa; Bouchard, Sébastien; Nkuranga, Martine; Bergeron, Michel G.; Rodriguez, Manuel J.

    2014-01-01

    This work demonstrates the ability of a bacterial concentration and recovery procedure combined with three different PCR assays targeting the lacZ, wecG, and 16S rRNA genes, respectively, to detect the presence of total coliforms in 100-ml samples of potable water (presence/absence test). PCR assays were first compared to the culture-based Colilert and MI agar methods to determine their ability to detect 147 coliform strains representing 76 species of Enterobacteriaceae encountered in fecal and environmental settings. Results showed that 86 (58.5%) and 109 (74.1%) strains yielded a positive signal with Colilert and MI agar methods, respectively, whereas the lacZ, wecG, and 16S rRNA PCR assays detected 133 (90.5%), 111 (75.5%), and 146 (99.3%) of the 147 total coliform strains tested. These assays were then assessed by testing 122 well water samples collected in the Québec City region of Canada. Results showed that 97 (79.5%) of the samples tested by culture-based methods and 95 (77.9%), 82 (67.2%), and 98 (80.3%) of samples tested using PCR-based methods contained total coliforms, respectively. Consequently, despite the high genetic variability of the total coliform group, this study demonstrated that it is possible to use molecular assays to detect total coliforms in potable water: the 16S rRNA molecular assay was shown to be as efficient as recommended culture-based methods. This assay might be used in combination with an Escherichia coli molecular assay to assess drinking water quality. PMID:24771030

  13. A novel sampling method for multiple multiscale targets from scattering amplitudes at a fixed frequency

    NASA Astrophysics Data System (ADS)

    Liu, Xiaodong

    2017-08-01

    A sampling method by using scattering amplitude is proposed for shape and location reconstruction in inverse acoustic scattering problems. Only matrix multiplication is involved in the computation, thus the novel sampling method is very easy and simple to implement. With the help of the factorization of the far field operator, we establish an inf-criterion for characterization of underlying scatterers. This result is then used to give a lower bound of the proposed indicator functional for sampling points inside the scatterers. While for the sampling points outside the scatterers, we show that the indicator functional decays like the bessel functions as the sampling point goes away from the boundary of the scatterers. We also show that the proposed indicator functional continuously depends on the scattering amplitude, this further implies that the novel sampling method is extremely stable with respect to errors in the data. Different to the classical sampling method such as the linear sampling method or the factorization method, from the numerical point of view, the novel indicator takes its maximum near the boundary of the underlying target and decays like the bessel functions as the sampling points go away from the boundary. The numerical simulations also show that the proposed sampling method can deal with multiple multiscale case, even the different components are close to each other.

  14. Method for Operating a Sensor to Differentiate Between Analytes in a Sample

    DOEpatents

    Kunt, Tekin; Cavicchi, Richard E; Semancik, Stephen; McAvoy, Thomas J

    1998-07-28

    Disclosed is a method for operating a sensor to differentiate between first and second analytes in a sample. The method comprises the steps of determining a input profile for the sensor which will enhance the difference in the output profiles of the sensor as between the first analyte and the second analyte; determining a first analyte output profile as observed when the input profile is applied to the sensor; determining a second analyte output profile as observed when the temperature profile is applied to the sensor; introducing the sensor to the sample while applying the temperature profile to the sensor, thereby obtaining a sample output profile; and evaluating the sample output profile as against the first and second analyte output profiles to thereby determine which of the analytes is present in the sample.

  15. Effects of sampling methods on the quantity and quality of dissolved organic matter in sediment pore waters as revealed by absorption and fluorescence spectroscopy.

    PubMed

    Chen, Meilian; Lee, Jong-Hyeon; Hur, Jin

    2015-10-01

    Despite literature evidence suggesting the importance of sampling methods on the properties of sediment pore waters, their effects on the dissolved organic matter (PW-DOM) have been unexplored to date. Here, we compared the effects of two commonly used sampling methods (i.e., centrifuge and Rhizon sampler) on the characteristics of PW-DOM for the first time. The bulk dissolved organic carbon (DOC), ultraviolet-visible (UV-Vis) absorption, and excitation-emission matrixes coupled with parallel factor analysis (EEM-PARAFAC) of the PW-DOM samples were compared for the two sampling methods with the sediments from minimal to severely contaminated sites. The centrifuged samples were found to have higher average values of DOC, UV absorption, and protein-like EEM-PARAFAC components. The samples collected with the Rhizon sampler, however, exhibited generally more humified characteristics than the centrifuged ones, implying a preferential collection of PW-DOM with respect to the sampling methods. Furthermore, the differences between the two sampling methods seem more pronounced in relatively more polluted sites. Our observations were possibly explained by either the filtration effect resulting from the smaller pore size of the Rhizon sampler or the desorption of DOM molecules loosely bound to minerals during centrifugation, or both. Our study suggests that consistent use of one sampling method is crucial for PW-DOM studies and also that caution should be taken in the comparison of data collected with different sampling methods.

  16. A novel method to handle the effect of uneven sampling effort in biodiversity databases.

    PubMed

    Pardo, Iker; Pata, María P; Gómez, Daniel; García, María B

    2013-01-01

    How reliable are results on spatial distribution of biodiversity based on databases? Many studies have evidenced the uncertainty related to this kind of analysis due to sampling effort bias and the need for its quantification. Despite that a number of methods are available for that, little is known about their statistical limitations and discrimination capability, which could seriously constrain their use. We assess for the first time the discrimination capacity of two widely used methods and a proposed new one (FIDEGAM), all based on species accumulation curves, under different scenarios of sampling exhaustiveness using Receiver Operating Characteristic (ROC) analyses. Additionally, we examine to what extent the output of each method represents the sampling completeness in a simulated scenario where the true species richness is known. Finally, we apply FIDEGAM to a real situation and explore the spatial patterns of plant diversity in a National Park. FIDEGAM showed an excellent discrimination capability to distinguish between well and poorly sampled areas regardless of sampling exhaustiveness, whereas the other methods failed. Accordingly, FIDEGAM values were strongly correlated with the true percentage of species detected in a simulated scenario, whereas sampling completeness estimated with other methods showed no relationship due to null discrimination capability. Quantifying sampling effort is necessary to account for the uncertainty in biodiversity analyses, however, not all proposed methods are equally reliable. Our comparative analysis demonstrated that FIDEGAM was the most accurate discriminator method in all scenarios of sampling exhaustiveness, and therefore, it can be efficiently applied to most databases in order to enhance the reliability of biodiversity analyses.

  17. A Novel Method to Handle the Effect of Uneven Sampling Effort in Biodiversity Databases

    PubMed Central

    Pardo, Iker; Pata, María P.; Gómez, Daniel; García, María B.

    2013-01-01

    How reliable are results on spatial distribution of biodiversity based on databases? Many studies have evidenced the uncertainty related to this kind of analysis due to sampling effort bias and the need for its quantification. Despite that a number of methods are available for that, little is known about their statistical limitations and discrimination capability, which could seriously constrain their use. We assess for the first time the discrimination capacity of two widely used methods and a proposed new one (FIDEGAM), all based on species accumulation curves, under different scenarios of sampling exhaustiveness using Receiver Operating Characteristic (ROC) analyses. Additionally, we examine to what extent the output of each method represents the sampling completeness in a simulated scenario where the true species richness is known. Finally, we apply FIDEGAM to a real situation and explore the spatial patterns of plant diversity in a National Park. FIDEGAM showed an excellent discrimination capability to distinguish between well and poorly sampled areas regardless of sampling exhaustiveness, whereas the other methods failed. Accordingly, FIDEGAM values were strongly correlated with the true percentage of species detected in a simulated scenario, whereas sampling completeness estimated with other methods showed no relationship due to null discrimination capability. Quantifying sampling effort is necessary to account for the uncertainty in biodiversity analyses, however, not all proposed methods are equally reliable. Our comparative analysis demonstrated that FIDEGAM was the most accurate discriminator method in all scenarios of sampling exhaustiveness, and therefore, it can be efficiently applied to most databases in order to enhance the reliability of biodiversity analyses. PMID:23326357

  18. Comparison of three sampling and analytical methods for the determination of airborne hexavalent chromium.

    PubMed

    Boiano, J M; Wallace, M E; Sieber, W K; Groff, J H; Wang, J; Ashley, K

    2000-08-01

    A field study was conducted with the goal of comparing the performance of three recently developed or modified sampling and analytical methods for the determination of airborne hexavalent chromium (Cr(VI)). The study was carried out in a hard chrome electroplating facility and in a jet engine manufacturing facility where airborne Cr(VI) was expected to be present. The analytical methods evaluated included two laboratory-based procedures (OSHA Method ID-215 and NIOSH Method 7605) and a field-portable method (NIOSH Method 7703). These three methods employ an identical sampling methodology: collection of Cr(VI)-containing aerosol on a polyvinyl chloride (PVC) filter housed in a sampling cassette, which is connected to a personal sampling pump calibrated at an appropriate flow rate. The basis of the analytical methods for all three methods involves extraction of the PVC filter in alkaline buffer solution, chemical isolation of the Cr(VI) ion, complexation of the Cr(VI) ion with 1,5-diphenylcarbazide, and spectrometric measurement of the violet chromium diphenylcarbazone complex at 540 nm. However, there are notable specific differences within the sample preparation procedures used in three methods. To assess the comparability of the three measurement protocols, a total of 20 side-by-side air samples were collected, equally divided between a chromic acid electroplating operation and a spray paint operation where water soluble forms of Cr(VI) were used. A range of Cr(VI) concentrations from 0.6 to 960 microg m(-3), with Cr(VI) mass loadings ranging from 0.4 to 32 microg, was measured at the two operations. The equivalence of the means of the log-transformed Cr(VI) concentrations obtained from the different analytical methods was compared. Based on analysis of variance (ANOVA) results, no statistically significant differences were observed between mean values measured using each of the three methods. Small but statistically significant differences were observed between

  19. Survey research with a random digit dial national mobile phone sample in Ghana: Methods and sample quality.

    PubMed

    L'Engle, Kelly; Sefa, Eunice; Adimazoya, Edward Akolgo; Yartey, Emmanuel; Lenzi, Rachel; Tarpo, Cindy; Heward-Mills, Nii Lante; Lew, Katherine; Ampeh, Yvonne

    2018-01-01

    Generating a nationally representative sample in low and middle income countries typically requires resource-intensive household level sampling with door-to-door data collection. High mobile phone penetration rates in developing countries provide new opportunities for alternative sampling and data collection methods, but there is limited information about response rates and sample biases in coverage and nonresponse using these methods. We utilized data from an interactive voice response, random-digit dial, national mobile phone survey in Ghana to calculate standardized response rates and assess representativeness of the obtained sample. The survey methodology was piloted in two rounds of data collection. The final survey included 18 demographic, media exposure, and health behavior questions. Call outcomes and response rates were calculated according to the American Association of Public Opinion Research guidelines. Sample characteristics, productivity, and costs per interview were calculated. Representativeness was assessed by comparing data to the Ghana Demographic and Health Survey and the National Population and Housing Census. The survey was fielded during a 27-day period in February-March 2017. There were 9,469 completed interviews and 3,547 partial interviews. Response, cooperation, refusal, and contact rates were 31%, 81%, 7%, and 39% respectively. Twenty-three calls were dialed to produce an eligible contact: nonresponse was substantial due to the automated calling system and dialing of many unassigned or non-working numbers. Younger, urban, better educated, and male respondents were overrepresented in the sample. The innovative mobile phone data collection methodology yielded a large sample in a relatively short period. Response rates were comparable to other surveys, although substantial coverage bias resulted from fewer women, rural, and older residents completing the mobile phone survey in comparison to household surveys. Random digit dialing of mobile

  20. Application of a Permethrin Immunosorbent Assay Method to Residential Soil and Dust Samples

    EPA Science Inventory

    A low-cost, high throughput bioanalytical screening method was developed for monitoring cis/trans-permethrin in dust and soil samples. The method consisted of a simple sample preparation procedure [sonication with dichloromethane followed by a solvent exchange into methanol:wate...

  1. Well purge and sample apparatus and method

    DOEpatents

    Schalla, Ronald; Smith, Ronald M.; Hall, Stephen H.; Smart, John E.; Gustafson, Gregg S.

    1995-01-01

    The present invention specifically permits purging and/or sampling of a well but only removing, at most, about 25% of the fluid volume compared to conventional methods and, at a minimum, removing none of the fluid volume from the well. The invention is an isolation assembly with a packer, pump and exhaust, that is inserted into the well. The isolation assembly is designed so that only a volume of fluid between the outside diameter of the isolation assembly and the inside diameter of the well over a fluid column height from the bottom of the well to the top of the active portion (lower annulus) is removed. The packer is positioned above the active portion thereby sealing the well and preventing any mixing or contamination of inlet fluid with fluid above the packer. Ports in the wall of the isolation assembly permit purging and sampling of the lower annulus along the height of the active portion.

  2. Well purge and sample apparatus and method

    DOEpatents

    Schalla, R.; Smith, R.M.; Hall, S.H.; Smart, J.E.; Gustafson, G.S.

    1995-10-24

    The present invention specifically permits purging and/or sampling of a well but only removing, at most, about 25% of the fluid volume compared to conventional methods and, at a minimum, removing none of the fluid volume from the well. The invention is an isolation assembly with a packer, pump and exhaust, that is inserted into the well. The isolation assembly is designed so that only a volume of fluid between the outside diameter of the isolation assembly and the inside diameter of the well over a fluid column height from the bottom of the well to the top of the active portion (lower annulus) is removed. The packer is positioned above the active portion thereby sealing the well and preventing any mixing or contamination of inlet fluid with fluid above the packer. Ports in the wall of the isolation assembly permit purging and sampling of the lower annulus along the height of the active portion. 8 figs.

  3. The Importance of Introductory Statistics Students Understanding Appropriate Sampling Techniques

    ERIC Educational Resources Information Center

    Menil, Violeta C.

    2005-01-01

    In this paper the author discusses the meaning of sampling, the reasons for sampling, the Central Limit Theorem, and the different techniques of sampling. Practical and relevant examples are given to make the appropriate sampling techniques understandable to students of Introductory Statistics courses. With a thorough knowledge of sampling…

  4. Prey Selection by an Apex Predator: The Importance of Sampling Uncertainty

    PubMed Central

    Davis, Miranda L.; Stephens, Philip A.; Willis, Stephen G.; Bassi, Elena; Marcon, Andrea; Donaggio, Emanuela; Capitani, Claudia; Apollonio, Marco

    2012-01-01

    The impact of predation on prey populations has long been a focus of ecologists, but a firm understanding of the factors influencing prey selection, a key predictor of that impact, remains elusive. High levels of variability observed in prey selection may reflect true differences in the ecology of different communities but might also reflect a failure to deal adequately with uncertainties in the underlying data. Indeed, our review showed that less than 10% of studies of European wolf predation accounted for sampling uncertainty. Here, we relate annual variability in wolf diet to prey availability and examine temporal patterns in prey selection; in particular, we identify how considering uncertainty alters conclusions regarding prey selection. Over nine years, we collected 1,974 wolf scats and conducted drive censuses of ungulates in Alpe di Catenaia, Italy. We bootstrapped scat and census data within years to construct confidence intervals around estimates of prey use, availability and selection. Wolf diet was dominated by boar (61.5±3.90 [SE] % of biomass eaten) and roe deer (33.7±3.61%). Temporal patterns of prey densities revealed that the proportion of roe deer in wolf diet peaked when boar densities were low, not when roe deer densities were highest. Considering only the two dominant prey types, Manly's standardized selection index using all data across years indicated selection for boar (mean = 0.73±0.023). However, sampling error resulted in wide confidence intervals around estimates of prey selection. Thus, despite considerable variation in yearly estimates, confidence intervals for all years overlapped. Failing to consider such uncertainty could lead erroneously to the assumption of differences in prey selection among years. This study highlights the importance of considering temporal variation in relative prey availability and accounting for sampling uncertainty when interpreting the results of dietary studies. PMID:23110122

  5. 40 CFR 80.8 - Sampling methods for gasoline and diesel fuel.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... applicable procedures specified in American Society for Testing and Materials (ASTM) method D 4057-95(2000... applicable procedures specified in ASTM method D 4177-95(2000), entitled “Standard Practice for Automatic... applicable procedures in ASTM method D 5842-95(2000), entitled “Standard Practice for Sampling and Handling...

  6. Rapid method to determine 89Sr/ 90Sr in large concrete samples

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Maxwell, Sherrod L.; Culligan, Brian; Hutchison, Jay B.

    Here, a new rapid method has been developed that provides high quality low-level measurements of 89,90Sr in concrete samples with an MDA (Minimum Detectable Activity) of <1 mBq g -1. The new method is fast, meets new decommissioning regulatory limits and is robust even if refractory particles are present. The method utilizes a rapid fusion to ensure total dissolution of samples and rapid preconcentration and separation of 89,90Sr from 5-10 g concrete samples. When, the 89Sr/ 90Sr ratio is high, Sr can be isolated from up to 5g concrete samples, total 89/90Sr measured, and then 90Sr determined via 90Y separatedmore » after a period of ingrowth. Another approach allows the immediate determination of 90Sr in 10 g concrete aliquots without waiting for 90Y ingrowth, in instances where the shorter lived 89Sr is unlikely to be encountered.« less

  7. Rapid method to determine 89Sr/ 90Sr in large concrete samples

    DOE PAGES

    Maxwell, Sherrod L.; Culligan, Brian; Hutchison, Jay B.; ...

    2016-03-24

    Here, a new rapid method has been developed that provides high quality low-level measurements of 89,90Sr in concrete samples with an MDA (Minimum Detectable Activity) of <1 mBq g -1. The new method is fast, meets new decommissioning regulatory limits and is robust even if refractory particles are present. The method utilizes a rapid fusion to ensure total dissolution of samples and rapid preconcentration and separation of 89,90Sr from 5-10 g concrete samples. When, the 89Sr/ 90Sr ratio is high, Sr can be isolated from up to 5g concrete samples, total 89/90Sr measured, and then 90Sr determined via 90Y separatedmore » after a period of ingrowth. Another approach allows the immediate determination of 90Sr in 10 g concrete aliquots without waiting for 90Y ingrowth, in instances where the shorter lived 89Sr is unlikely to be encountered.« less

  8. [4D-MRI using the synchronized sampling method (SSM)].

    PubMed

    Shimada, Yasuhiro; Fujimoto, Ichirou; Takemoto, Hironori; Takano, Sayoko; Masaki, Shinobu; Honda, Kiyoshi; Takeo, Kazuhiro

    2002-12-01

    A synchronized sampling method (SSM) was developed for the study of voluntary movements by combining the electrocardiographic (ECG) gating method with an external triggering device, and four-dimensional magnetic resonance imaging (4D-MRI) at a rate of 30 frames per second was accomplished by volumetric imaging with the SSM. This method was first applied to the motion imaging of articulatory organs during repetitions of a Japanese five-vowel sequence, and the dynamic change in vocal tract area function was demonstrated with sufficient temporal resolution. This paper describes the methodology, applicability, and limitations of 4D-MRI with the SSM.

  9. A comparison of four sampling methods among men having sex with men in China: implications for HIV/STD surveillance and prevention.

    PubMed

    Guo, Yan; Li, Xiaoming; Fang, Xiaoyi; Lin, Xiuyun; Song, Yan; Jiang, Shuling; Stanton, Bonita

    2011-11-01

    Sample representativeness remains one of the challenges in effective HIV/STD surveillance and prevention targeting men who have sex with men (MSM) worldwide. Although convenience samples are widely used in studies of MSM, previous studies suggested that these samples might not be representative of the broader MSM population. This issue becomes even more critical in many developing countries where needed resources for conducting probability sampling are limited. We examined variations in HIV and Syphilis infections and sociodemographic and behavioral factors among 307 young migrant MSM recruited using four different convenience sampling methods (peer outreach, informal social network, Internet, and venue-based) in Beijing, China in 2009. The participants completed a self-administered survey and provided blood specimens for HIV/STD testing. Among the four MSM samples using different recruitment methods, rates of HIV infections were 5.1%, 5.8%, 7.8%, and 3.4%; rates of Syphilis infection were 21.8%, 36.2%, 11.8%, and 13.8%; and rates of inconsistent condom use were 57%, 52%, 58%, and 38%. Significant differences were found in various sociodemographic characteristics (e.g., age, migration history, education, income, and places of employment) and risk behaviors (e.g., age at first sex, number of sex partners, involvement in commercial sex, and substance use) among samples recruited by different sampling methods. The results confirmed the challenges of obtaining representative MSM samples and underscored the importance of using multiple sampling methods to reach MSM from diverse backgrounds and in different social segments and to improve the representativeness of the MSM samples when the use of probability sampling approach is not feasible.

  10. A Lipid Extraction and Analysis Method for Characterizing Soil Microbes in Experiments with Many Samples

    PubMed Central

    Oates, Lawrence G.; Read, Harry W.; Gutknecht, Jessica L. M.; Duncan, David S.; Balser, Teri B.; Jackson, Randall D.

    2017-01-01

    Microbial communities are important drivers and regulators of ecosystem processes. To understand how management of ecosystems may affect microbial communities, a relatively precise but effort-intensive technique to assay microbial community composition is phospholipid fatty acid (PLFA) analysis. PLFA was developed to analyze phospholipid biomarkers, which can be used as indicators of microbial biomass and the composition of broad functional groups of fungi and bacteria. It has commonly been used to compare soils under alternative plant communities, ecology, and management regimes. The PLFA method has been shown to be sensitive to detecting shifts in microbial community composition. An alternative method, fatty acid methyl ester extraction and analysis (MIDI-FA) was developed for rapid extraction of total lipids, without separation of the phospholipid fraction, from pure cultures as a microbial identification technique. This method is rapid but is less suited for soil samples because it lacks an initial step separating soil particles and begins instead with a saponification reaction that likely produces artifacts from the background organic matter in the soil. This article describes a method that increases throughput while balancing effort and accuracy for extraction of lipids from the cell membranes of microorganisms for use in characterizing both total lipids and the relative abundance of indicator lipids to determine soil microbial community structure in studies with many samples. The method combines the accuracy achieved through PLFA profiling by extracting and concentrating soil lipids as a first step, and a reduction in effort by saponifying the organic material extracted and processing with the MIDI-FA method as a second step. PMID:28745639

  11. The model of flood control using servqual method and importance performance analysis in Surakarta City – Indonesia

    NASA Astrophysics Data System (ADS)

    Titi Purwantini, V.; Sutanto, Yusuf

    2018-05-01

    This research is to create a model of flood control in the city of Surakarta using Servqual method and Importance Performance Analysis. Service quality is generally defined as the overall assessment of a service by the customersor the extent to which a service meets customer’s needs or expectations. The purpose of this study is to find the first model of flood control that is appropriate to the condition of the community. Surakarta This means looking for a model that can provide satisfactory service for the people of Surakarta who are in the location of the flood. The second is to find the right model to improve service performance of Surakarta City Government in serving the people in flood location. The method used to determine the satisfaction of the public on the quality of service is to see the difference in the quality of service expected by the community with the reality. This method is Servqual Method While to assess the performance of city government officials is by comparing the actual performance with the quality of services provided, this method is This means looking for a model that can provide satisfactory service for the people of Surakarta who are in the location of the flood.The second is to find the right model to improve service performance of Surakarta City Government in serving the people in flood location. The method used to determine the satisfaction of the public on the quality of service is to see the difference in the quality of service expected by the community with the reality. This method is Servqual Method While to assess the performance of city government officials is by comparing the actual performance with the quality of services provided, this method is Importance Performance Analysis. Samples were people living in flooded areas in the city of Surakarta. Result this research is Satisfaction = Responsiveness+ Realibility + Assurance + Empathy+ Tangible (Servqual Model) and Importance Performance Analysis is From Cartesian diagram

  12. Quality of omeprazole purchased via the Internet and personally imported into Japan: comparison with products sampled in other Asian countries.

    PubMed

    Rahman, Mohammad Sofiqur; Yoshida, Naoko; Sugiura, Sakura; Tsuboi, Hirohito; Keila, Tep; Kiet, Heng Bun; Zin, Theingi; Tanimoto, Tsuyoshi; Kimura, Kazuko

    2018-03-01

    To evaluate the quality of omeprazole personally imported into Japan via the Internet and to compare the quality of these samples with previously collected samples from two other Asian countries. The samples were evaluated by observation, authenticity investigation and pharmacopoeial quality analysis. Quality comparison of some selected samples was carried out by dissolution profiling, Raman spectroscopy and principle component analysis (PCA). Observation of the Internet sites and samples revealed some discrepancies including the delivery of a wrong sample and the selling of omeprazole without a prescription, although it is a prescription medicine. Among the 28 samples analysed, all passed the identification test, 26 (93%) passed the quantity and content uniformity tests and all passed the dissolution test. Dissolution profiling confirmed that all the personally imported omeprazole samples remained intact in the acid medium. On the other hand, six samples from two of the same manufacturers, previously collected during surveys in Cambodia and Myanmar, frequently showed premature omeprazole release in acid. Raman spectroscopy and PCA showed significant variation between omeprazole formulations in personally imported samples and the samples from Cambodia and Myanmar. Our results indicate that the pharmaceutical quality of omeprazole purchased through the Internet was sufficient, as determined by pharmacopeial tests. However, omeprazole formulations distributed in different market segments by the same manufacturers were of diverse quality. Measures are needed to ensure consistent quality of products and to prevent entry of substandard products into the legitimate supply chain. © 2018 The Authors. Tropical Medicine & International Health Published by John Wiley & Sons Ltd.

  13. Impact of culture media and sampling methods on Staphylococcus aureus aerosols.

    PubMed

    Chang, C-W; Wang, L-J

    2015-10-01

    Staphylococcus aureus has been detected indoors and is associated with human infection. Reliable quantification of S. aureus using a sampling technique followed by culture assay helps in assessing the risks of human exposure. The efficiency of five culture media and eight sampling methods in recovering S. aureus aerosols were evaluated. Methods to extract cells from filters were also studied. Tryptic soy agar (TSA) presented greater bacterial recovery than mannitol salt agar (MSA), CHROMagar staph aureus, Chapman stone medium, and Baird-Park agarose (P < 0.05). Moreover, 93 ± 2%-95 ± 2% and 42 ± 1%-49 ± 2% of S. aureus were, respectively, recovered by a 15-min heating of gelatin filters and 2-min vortex of polycarbonate (PC) filters. Evaluation of two filtration (IOM with gelatin filter and cassette with PC filter), two impaction (Andersen 1-STG loaded with TSA and MSA) and four impingement methods [AGI-30 and BioSampler filled with Tween mixture (TM) and phosphate-buffered saline (PBS)] revealed the BioSampler/TM performed best over 30 and 60 min of sampling (P < 0.05), while low recovery efficiencies were associated with the IOM/gelatin, cassette/PC, and AGI-30/PBS combinations (P < 0.05). In addition to BioSampler/TM, collecting S. aureus onto TSA from the Andersen 1-STG is also recommended, as it is the second best method at the 60-min sampling (P < 0.05). © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  14. Duplex sampling apparatus and method

    DOEpatents

    Brown, Paul E.; Lloyd, Robert

    1992-01-01

    An improved apparatus is provided for sampling a gaseous mixture and for measuring mixture components. The apparatus includes two sampling containers connected in series serving as a duplex sampling apparatus. The apparatus is adapted to independently determine the amounts of condensable and noncondensable gases in admixture from a single sample. More specifically, a first container includes a first port capable of selectively connecting to and disconnecting from a sample source and a second port capable of selectively connecting to and disconnecting from a second container. A second container also includes a first port capable of selectively connecting to and disconnecting from the second port of the first container and a second port capable of either selectively connecting to and disconnecting from a differential pressure source. By cooling a mixture sample in the first container, the condensable vapors form a liquid, leaving noncondensable gases either as free gases or dissolved in the liquid. The condensed liquid is heated to drive out dissolved noncondensable gases, and all the noncondensable gases are transferred to the second container. Then the first and second containers are separated from one another in order to separately determine the amount of noncondensable gases and the amount of condensable gases in the sample.

  15. Methods, compounds and systems for detecting a microorganism in a sample

    DOEpatents

    Colston, Jr, Bill W.; Fitch, J. Patrick; Gardner, Shea N.; Williams, Peter L.; Wagner, Mark C.

    2016-09-06

    Methods to identify a set of probe polynucleotides suitable for detecting a set of targets and in particular methods for identification of primers suitable for detection of target microorganisms related polynucleotides, set of polynucleotides and compositions, and related methods and systems for detection and/or identification of microorganisms in a sample.

  16. Note: A simple image processing based fiducial auto-alignment method for sample registration.

    PubMed

    Robertson, Wesley D; Porto, Lucas R; Ip, Candice J X; Nantel, Megan K T; Tellkamp, Friedjof; Lu, Yinfei; Miller, R J Dwayne

    2015-08-01

    A simple method for the location and auto-alignment of sample fiducials for sample registration using widely available MATLAB/LabVIEW software is demonstrated. The method is robust, easily implemented, and applicable to a wide variety of experiment types for improved reproducibility and increased setup speed. The software uses image processing to locate and measure the diameter and center point of circular fiducials for distance self-calibration and iterative alignment and can be used with most imaging systems. The method is demonstrated to be fast and reliable in locating and aligning sample fiducials, provided here by a nanofabricated array, with accuracy within the optical resolution of the imaging system. The software was further demonstrated to register, load, and sample the dynamically wetted array.

  17. Final Report for X-ray Diffraction Sample Preparation Method Development

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ely, T. M.; Meznarich, H. K.; Valero, T.

    WRPS-1500790, “X-ray Diffraction Saltcake Sample Preparation Method Development Plan/Procedure,” was originally prepared with the intent of improving the specimen preparation methodology used to generate saltcake specimens suitable for XRD-based solid phase characterization. At the time that this test plan document was originally developed, packed powder in cavity supports with collodion binder was the established XRD specimen preparation method. An alternate specimen preparation method less vulnerable, if not completely invulnerable to preferred orientation effects, was desired as a replacement for the method.

  18. Evaluation of an alternate method for sampling benthic macroinvertebrates in low-gradient streams sampled as part of the National Rivers and Streams Assessment.

    PubMed

    Flotemersch, Joseph E; North, Sheila; Blocksom, Karen A

    2014-02-01

    Benthic macroinvertebrates are sampled in streams and rivers as one of the assessment elements of the US Environmental Protection Agency's National Rivers and Streams Assessment. In a 2006 report, the recommendation was made that different yet comparable methods be evaluated for different types of streams (e.g., low gradient vs. high gradient). Consequently, a research element was added to the 2008-2009 National Rivers and Streams Assessment to conduct a side-by-side comparison of the standard macroinvertebrate sampling method with an alternate method specifically designed for low-gradient wadeable streams and rivers that focused more on stream edge habitat. Samples were collected using each method at 525 sites in five of nine aggregate ecoregions located in the conterminous USA. Methods were compared using the benthic macroinvertebrate multimetric index developed for the 2006 Wadeable Streams Assessment. Statistical analysis did not reveal any trends that would suggest the overall assessment of low-gradient streams on a regional or national scale would change if the alternate method was used rather than the standard sampling method, regardless of the gradient cutoff used to define low-gradient streams. Based on these results, the National Rivers and Streams Survey should continue to use the standard field method for sampling all streams.

  19. Methods of human body odor sampling: the effect of freezing.

    PubMed

    Lenochova, Pavlina; Roberts, S Craig; Havlicek, Jan

    2009-02-01

    Body odor sampling is an essential tool in human chemical ecology research. However, methodologies of individual studies vary widely in terms of sampling material, length of sampling, and sample processing. Although these differences might have a critical impact on results obtained, almost no studies test validity of current methods. Here, we focused on the effect of freezing samples between collection and use in experiments involving body odor perception. In 2 experiments, we tested whether axillary odors were perceived differently by raters when presented fresh or having been frozen and whether several freeze-thaw cycles affected sample quality. In the first experiment, samples were frozen for 2 weeks, 1 month, or 4 months. We found no differences in ratings of pleasantness, attractiveness, or masculinity between fresh and frozen samples. Similarly, almost no differences between repeatedly thawed and fresh samples were found. We found some variations in intensity; however, this was unrelated to length of storage. The second experiment tested differences between fresh samples and those frozen for 6 months. Again no differences in subjective ratings were observed. These results suggest that freezing has no significant effect on perceived odor hedonicity and that samples can be reliably used after storage for relatively long periods.

  20. Molecular method for detection of total coliforms in drinking water samples.

    PubMed

    Maheux, Andrée F; Boudreau, Dominique K; Bisson, Marc-Antoine; Dion-Dupont, Vanessa; Bouchard, Sébastien; Nkuranga, Martine; Bergeron, Michel G; Rodriguez, Manuel J

    2014-07-01

    This work demonstrates the ability of a bacterial concentration and recovery procedure combined with three different PCR assays targeting the lacZ, wecG, and 16S rRNA genes, respectively, to detect the presence of total coliforms in 100-ml samples of potable water (presence/absence test). PCR assays were first compared to the culture-based Colilert and MI agar methods to determine their ability to detect 147 coliform strains representing 76 species of Enterobacteriaceae encountered in fecal and environmental settings. Results showed that 86 (58.5%) and 109 (74.1%) strains yielded a positive signal with Colilert and MI agar methods, respectively, whereas the lacZ, wecG, and 16S rRNA PCR assays detected 133 (90.5%), 111 (75.5%), and 146 (99.3%) of the 147 total coliform strains tested. These assays were then assessed by testing 122 well water samples collected in the Québec City region of Canada. Results showed that 97 (79.5%) of the samples tested by culture-based methods and 95 (77.9%), 82 (67.2%), and 98 (80.3%) of samples tested using PCR-based methods contained total coliforms, respectively. Consequently, despite the high genetic variability of the total coliform group, this study demonstrated that it is possible to use molecular assays to detect total coliforms in potable water: the 16S rRNA molecular assay was shown to be as efficient as recommended culture-based methods. This assay might be used in combination with an Escherichia coli molecular assay to assess drinking water quality. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  1. Persistent Organic Pollutant Determination in Killer Whale Scat Samples: Optimization of a Gas Chromatography/Mass Spectrometry Method and Application to Field Samples.

    PubMed

    Lundin, Jessica I; Dills, Russell L; Ylitalo, Gina M; Hanson, M Bradley; Emmons, Candice K; Schorr, Gregory S; Ahmad, Jacqui; Hempelmann, Jennifer A; Parsons, Kim M; Wasser, Samuel K

    2016-01-01

    Biologic sample collection in wild cetacean populations is challenging. Most information on toxicant levels is obtained from blubber biopsy samples; however, sample collection is invasive and strictly regulated under permit, thus limiting sample numbers. Methods are needed to monitor toxicant levels that increase temporal and repeat sampling of individuals for population health and recovery models. The objective of this study was to optimize measuring trace levels (parts per billion) of persistent organic pollutants (POPs), namely polychlorinated-biphenyls (PCBs), polybrominated-diphenyl-ethers (PBDEs), dichlorodiphenyltrichloroethanes (DDTs), and hexachlorocyclobenzene, in killer whale scat (fecal) samples. Archival scat samples, initially collected, lyophilized, and extracted with 70 % ethanol for hormone analyses, were used to analyze POP concentrations. The residual pellet was extracted and analyzed using gas chromatography coupled with mass spectrometry. Method detection limits ranged from 11 to 125 ng/g dry weight. The described method is suitable for p,p'-DDE, PCBs-138, 153, 180, and 187, and PBDEs-47 and 100; other POPs were below the limit of detection. We applied this method to 126 scat samples collected from Southern Resident killer whales. Scat samples from 22 adult whales also had known POP concentrations in blubber and demonstrated significant correlations (p < 0.01) between matrices across target analytes. Overall, the scat toxicant measures matched previously reported patterns from blubber samples of decreased levels in reproductive-age females and a decreased p,p'-DDE/∑PCB ratio in J-pod. Measuring toxicants in scat samples provides an unprecedented opportunity to noninvasively evaluate contaminant levels in wild cetacean populations; these data have the prospect to provide meaningful information for vital management decisions.

  2. The effect of sampling techniques used in the multiconfigurational Ehrenfest method

    NASA Astrophysics Data System (ADS)

    Symonds, C.; Kattirtzi, J. A.; Shalashilin, D. V.

    2018-05-01

    In this paper, we compare and contrast basis set sampling techniques recently developed for use in the ab initio multiple cloning method, a direct dynamics extension to the multiconfigurational Ehrenfest approach, used recently for the quantum simulation of ultrafast photochemistry. We demonstrate that simultaneous use of basis set cloning and basis function trains can produce results which are converged to the exact quantum result. To demonstrate this, we employ these sampling methods in simulations of quantum dynamics in the spin boson model with a broad range of parameters and compare the results to accurate benchmarks.

  3. The effect of sampling techniques used in the multiconfigurational Ehrenfest method.

    PubMed

    Symonds, C; Kattirtzi, J A; Shalashilin, D V

    2018-05-14

    In this paper, we compare and contrast basis set sampling techniques recently developed for use in the ab initio multiple cloning method, a direct dynamics extension to the multiconfigurational Ehrenfest approach, used recently for the quantum simulation of ultrafast photochemistry. We demonstrate that simultaneous use of basis set cloning and basis function trains can produce results which are converged to the exact quantum result. To demonstrate this, we employ these sampling methods in simulations of quantum dynamics in the spin boson model with a broad range of parameters and compare the results to accurate benchmarks.

  4. Validated method for quantification of genetically modified organisms in samples of maize flour.

    PubMed

    Kunert, Renate; Gach, Johannes S; Vorauer-Uhl, Karola; Engel, Edwin; Katinger, Hermann

    2006-02-08

    Sensitive and accurate testing for trace amounts of biotechnology-derived DNA from plant material is the prerequisite for detection of 1% or 0.5% genetically modified ingredients in food products or raw materials thereof. Compared to ELISA detection of expressed proteins, real-time PCR (RT-PCR) amplification has easier sample preparation and detection limits are lower. Of the different methods of DNA preparation CTAB method with high flexibility in starting material and generation of sufficient DNA with relevant quality was chosen. Previous RT-PCR data generated with the SYBR green detection method showed that the method is highly sensitive to sample matrices and genomic DNA content influencing the interpretation of results. Therefore, this paper describes a real-time DNA quantification based on the TaqMan probe method, indicating high accuracy and sensitivity with detection limits of lower than 18 copies per sample applicable and comparable to highly purified plasmid standards as well as complex matrices of genomic DNA samples. The results were evaluated with ValiData for homology of variance, linearity, accuracy of the standard curve, and standard deviation.

  5. Collection of Oral Fluids Using Cotton Ropes as a Sampling Method to Detect Foot-and-Mouth Disease Virus Infection in Pigs.

    PubMed

    Vosloo, W; Morris, J; Davis, A; Giles, M; Wang, J; Nguyen, H T T; Kim, P V; Quach, N V; Le, P T T; Nguyen, P H N; Dang, H; Tran, H X; Vu, P P; Hung, V V; Le, Q T; Tran, T M; Mai, T M T; Le, Q T V; Singanallur, N B

    2015-10-01

    In high-density farming practices, it is important to constantly monitor for infectious diseases, especially diseases that have the potential to spread rapidly between holdings. Pigs are known to amplify foot-and-mouth disease (FMD) by excreting large amounts of virus, and it is therefore important to detect the virus quickly and accurately to minimize the spread of disease. Ropes were used to collect oral fluid samples from pigs, and each sample was compared to saliva samples collected from individual animals by detecting FMD virus RNA using real-time PCR. Two different experiments are described where groups of pigs were infected with different serotypes of FMD virus, either with or without vaccination, and unvaccinated pigs were kept in aerosol contact. The sensitivity of the rope sampling varied between 0.67 and 0.92, and the statistical agreement between this method and individual sampling ranged from substantial to moderate for the two different serotypes. The ease of collecting oral fluids using ropes together with the high sensitivity of subsequent FMD detection through PCR indicates that this could be a useful method to monitor pig populations for FMD virus infection. With further validation of the sensitivity of detection of FMD virus RNA, this can be a cost-effective, non-invasive diagnostic tool. © 2013 Blackwell Verlag GmbH.

  6. An improved SRC method based on virtual samples for face recognition

    NASA Astrophysics Data System (ADS)

    Fu, Lijun; Chen, Deyun; Lin, Kezheng; Li, Ao

    2018-07-01

    The sparse representation classifier (SRC) performs classification by evaluating which class leads to the minimum representation error. However, in real world, the number of available training samples is limited due to noise interference, training samples cannot accurately represent the test sample linearly. Therefore, in this paper, we first produce virtual samples by exploiting original training samples at the aim of increasing the number of training samples. Then, we take the intra-class difference as data representation of partial noise, and utilize the intra-class differences and training samples simultaneously to represent the test sample in a linear way according to the theory of SRC algorithm. Using weighted score level fusion, the respective representation scores of the virtual samples and the original training samples are fused together to obtain the final classification results. The experimental results on multiple face databases show that our proposed method has a very satisfactory classification performance.

  7. Autonomous spatially adaptive sampling in experiments based on curvature, statistical error and sample spacing with applications in LDA measurements

    NASA Astrophysics Data System (ADS)

    Theunissen, Raf; Kadosh, Jesse S.; Allen, Christian B.

    2015-06-01

    Spatially varying signals are typically sampled by collecting uniformly spaced samples irrespective of the signal content. For signals with inhomogeneous information content, this leads to unnecessarily dense sampling in regions of low interest or insufficient sample density at important features, or both. A new adaptive sampling technique is presented directing sample collection in proportion to local information content, capturing adequately the short-period features while sparsely sampling less dynamic regions. The proposed method incorporates a data-adapted sampling strategy on the basis of signal curvature, sample space-filling, variable experimental uncertainty and iterative improvement. Numerical assessment has indicated a reduction in the number of samples required to achieve a predefined uncertainty level overall while improving local accuracy for important features. The potential of the proposed method has been further demonstrated on the basis of Laser Doppler Anemometry experiments examining the wake behind a NACA0012 airfoil and the boundary layer characterisation of a flat plate.

  8. Comparison of indoor air sampling and dust collection methods for fungal exposure assessment using quantitative PCR

    EPA Science Inventory

    Evaluating fungal contamination indoors is complicated because of the many different sampling methods utilized. In this study, fungal contamination was evaluated using five sampling methods and four matrices for results. The five sampling methods were a 48 hour indoor air sample ...

  9. Probe Heating Method for the Analysis of Solid Samples Using a Portable Mass Spectrometer

    PubMed Central

    Kumano, Shun; Sugiyama, Masuyuki; Yamada, Masuyoshi; Nishimura, Kazushige; Hasegawa, Hideki; Morokuma, Hidetoshi; Inoue, Hiroyuki; Hashimoto, Yuichiro

    2015-01-01

    We previously reported on the development of a portable mass spectrometer for the onsite screening of illicit drugs, but our previous sampling system could only be used for liquid samples. In this study, we report on an attempt to develop a probe heating method that also permits solid samples to be analyzed using a portable mass spectrometer. An aluminum rod is used as the sampling probe. The powdered sample is affixed to the sampling probe or a droplet of sample solution is placed on the tip of the probe and dried. The probe is then placed on a heater to vaporize the sample. The vapor is then introduced into the portable mass spectrometer and analyzed. With the heater temperature set to 130°C, the developed system detected 1 ng of methamphetamine, 1 ng of amphetamine, 3 ng of 3,4-methylenedioxymethamphetamine, 1 ng of 3,4-methylenedioxyamphetamine, and 0.3 ng of cocaine. Even from mixtures consisting of clove powder and methamphetamine powder, methamphetamine ions were detected by tandem mass spectrometry. The developed probe heating method provides a simple method for the analysis of solid samples. A portable mass spectrometer incorporating this method would thus be useful for the onsite screening of illicit drugs. PMID:26819909

  10. A novel sample preparation method using rapid nonheated saponification method for the determination of cholesterol in emulsified foods.

    PubMed

    Jeong, In-Seek; Kwak, Byung-Man; Ahn, Jang-Hyuk; Leem, Donggil; Yoon, Taehyung; Yoon, Changyong; Jeong, Jayoung; Park, Jung-Min; Kim, Jin-Man

    2012-10-01

    In this study, nonheated saponification was employed as a novel, rapid, and easy sample preparation method for the determination of cholesterol in emulsified foods. Cholesterol content was analyzed using gas chromatography with a flame ionization detector (GC-FID). The cholesterol extraction method was optimized for maximum recovery from baby food and infant formula. Under these conditions, the optimum extraction solvent was 10 mL ethyl ether per 1 to 2 g sample, and the saponification solution was 0.2 mL KOH in methanol. The cholesterol content in the products was determined to be within the certified range of certified reference materials (CRMs), NIST SRM 1544 and SRM 1849. The results of the recovery test performed using spiked materials were in the range of 98.24% to 99.45% with an relative standard devitation (RSD) between 0.83% and 1.61%. This method could be used to reduce sample pretreatment time and is expected to provide an accurate determination of cholesterol in emulsified food matrices such as infant formula and baby food. A novel, rapid, and easy sample preparation method using nonheated saponification was developed for cholesterol detection in emulsified foods. Recovery tests of CRMs were satisfactory, and the recoveries of spiked materials were accurate and precise. This method was effective and decreased the time required for analysis by 5-fold compared to the official method. © 2012 Institute of Food Technologists®

  11. METHOD FOR MICRORNA ISOLATION FROM CLINICAL SERUM SAMPLES

    PubMed Central

    Li, Yu; Kowdley, Kris V.

    2012-01-01

    MicroRNAs are a group of intracellular non-coding RNA molecules that have been implicated in a variety of human diseases. Due to their high stability in blood, microRNAs released into circulation could be potentially utilized as non-invasive biomarkers for diagnosis or prognosis. Current microRNA isolation protocols are specifically designed for solid tissues and are impractical for biomarker development utilizing small-volume serum samples on a large scale. Thus, a protocol for microRNA isolation from serum is needed to accommodate these conditions in biomarker development. To establish such a protocol, we developed a simplified approach to normalize sample input by using single synthetic spike-in microRNA. We evaluated three commonly used commercial microRNA isolation kits for the best performance by comparing RNA quality and yield. The manufacturer’s protocol was further modified to improve the microRNA yield from 200 μL of human serum. MicroRNAs isolated from a large set of clinical serum samples were tested on the miRCURY LNA real-time PCR panel and confirmed to be suitable for high-throughput microRNA profiling. In conclusion, we have established a proven method for microRNA isolation from clinical serum samples suitable for microRNA biomarker development. PMID:22982505

  12. Multivariate Methods for Prediction of Geologic Sample Composition with Laser-Induced Breakdown Spectroscopy

    NASA Technical Reports Server (NTRS)

    Morris, Richard; Anderson, R.; Clegg, S. M.; Bell, J. F., III

    2010-01-01

    Laser-induced breakdown spectroscopy (LIBS) uses pulses of laser light to ablate a material from the surface of a sample and produce an expanding plasma. The optical emission from the plasma produces a spectrum which can be used to classify target materials and estimate their composition. The ChemCam instrument on the Mars Science Laboratory (MSL) mission will use LIBS to rapidly analyze targets remotely, allowing more resource- and time-intensive in-situ analyses to be reserved for targets of particular interest. ChemCam will also be used to analyze samples that are not reachable by the rover's in-situ instruments. Due to these tactical and scientific roles, it is important that ChemCam-derived sample compositions are as accurate as possible. We have compared the results of partial least squares (PLS), multilayer perceptron (MLP) artificial neural networks (ANNs), and cascade correlation (CC) ANNs to determine which technique yields better estimates of quantitative element abundances in rock and mineral samples. The number of hidden nodes in the MLP ANNs was optimized using a genetic algorithm. The influence of two data preprocessing techniques were also investigated: genetic algorithm feature selection and averaging the spectra for each training sample prior to training the PLS and ANN algorithms. We used a ChemCam-like laboratory stand-off LIBS system to collect spectra of 30 pressed powder geostandards and a diverse suite of 196 geologic slab samples of known bulk composition. We tested the performance of PLS and ANNs on a subset of these samples, choosing to focus on silicate rocks and minerals with a loss on ignition of less than 2 percent. This resulted in a set of 22 pressed powder geostandards and 80 geologic samples. Four of the geostandards were used as a validation set and 18 were used as the training set for the algorithms. We found that PLS typically resulted in the lowest average absolute error in its predictions, but that the optimized MLP ANN and

  13. Method to make accurate concentration and isotopic measurements for small gas samples

    NASA Astrophysics Data System (ADS)

    Palmer, M. R.; Wahl, E.; Cunningham, K. L.

    2013-12-01

    Carbon isotopic ratio measurements of CO2 and CH4 provide valuable insight into carbon cycle processes. However, many of these studies, like soil gas, soil flux, and water head space experiments, provide very small gas sample volumes, too small for direct measurement by current constant-flow Cavity Ring-Down (CRDS) isotopic analyzers. Previously, we addressed this issue by developing a sample introduction module which enabled the isotopic ratio measurement of 40ml samples or smaller. However, the system, called the Small Sample Isotope Module (SSIM), does dilute the sample during the delivery with inert carrier gas which causes a ~5% reduction in concentration. The isotopic ratio measurements are not affected by this small dilution, but researchers are naturally interested accurate concentration measurements. We present the accuracy and precision of a new method of using this delivery module which we call 'double injection.' Two portions of the 40ml of the sample (20ml each) are introduced to the analyzer, the first injection of which flushes out the diluting gas and the second injection is measured. The accuracy of this new method is demonstrated by comparing the concentration and isotopic ratio measurements for a gas sampled directly and that same gas measured through the SSIM. The data show that the CO2 concentration measurements were the same within instrument precision. The isotopic ratio precision (1σ) of repeated measurements was 0.16 permil for CO2 and 1.15 permil for CH4 at ambient concentrations. This new method provides a significant enhancement in the information provided by small samples.

  14. Molecular analyses of two bacterial sampling methods in ligature-induced periodontitis in rats.

    PubMed

    Fontana, Carla Raquel; Grecco, Clovis; Bagnato, Vanderlei Salvador; de Freitas, Laura Marise; Boussios, Constantinos I; Soukos, Nikolaos S

    2018-02-01

    The prevalence profile of periodontal pathogens in dental plaque can vary as a function of the detection method; however, the sampling technique may also play a role in determining dental plaque microbial profiles. We sought to determine the bacterial composition comparing two sampling methods, one well stablished and a new one proposed here. In this study, a ligature-induced periodontitis model was used in 30 rats. Twenty-seven days later, ligatures were removed and microbiological samples were obtained directly from the ligatures as well as from the periodontal pockets using absorbent paper points. Microbial analysis was performed using DNA probes to a panel of 40 periodontal species in the checkerboard assay. The bacterial composition patterns were similar for both sampling methods. However, detection levels for all species were markedly higher for ligatures compared with paper points. Ligature samples provided more bacterial counts than paper points, suggesting that the technique for induction of periodontitis could also be applied for sampling in rats. Our findings may be helpful in designing studies of induced periodontal disease-associated microbiota.

  15. Eigenvector method for umbrella sampling enables error analysis

    PubMed Central

    Thiede, Erik H.; Van Koten, Brian; Weare, Jonathan; Dinner, Aaron R.

    2016-01-01

    Umbrella sampling efficiently yields equilibrium averages that depend on exploring rare states of a model by biasing simulations to windows of coordinate values and then combining the resulting data with physical weighting. Here, we introduce a mathematical framework that casts the step of combining the data as an eigenproblem. The advantage to this approach is that it facilitates error analysis. We discuss how the error scales with the number of windows. Then, we derive a central limit theorem for averages that are obtained from umbrella sampling. The central limit theorem suggests an estimator of the error contributions from individual windows, and we develop a simple and computationally inexpensive procedure for implementing it. We demonstrate this estimator for simulations of the alanine dipeptide and show that it emphasizes low free energy pathways between stable states in comparison to existing approaches for assessing error contributions. Our work suggests the possibility of using the estimator and, more generally, the eigenvector method for umbrella sampling to guide adaptation of the simulation parameters to accelerate convergence. PMID:27586912

  16. Cytotoxicity of Light-Cured Dental Materials according to Different Sample Preparation Methods

    PubMed Central

    Lee, Myung-Jin; Kim, Mi-Joo; Kwon, Jae-Sung; Lee, Sang-Bae; Kim, Kwang-Mahn

    2017-01-01

    Dental light-cured resins can undergo different degrees of polymerization when applied in vivo. When polymerization is incomplete, toxic monomers may be released into the oral cavity. The present study assessed the cytotoxicity of different materials, using sample preparation methods that mirror clinical conditions. Composite and bonding resins were used and divided into four groups according to sample preparation method: uncured; directly cured samples, which were cured after being placed on solidified agar; post-cured samples were polymerized before being placed on agar; and “removed unreacted layer” samples had their oxygen-inhibition layer removed after polymerization. Cytotoxicity was evaluated using an agar diffusion test, MTT assay, and confocal microscopy. Uncured samples were the most cytotoxic, while removed unreacted layer samples were the least cytotoxic (p < 0.05). In the MTT assay, cell viability increased significantly in every group as the concentration of the extracts decreased (p < 0.05). Extracts from post-cured and removed unreacted layer samples of bonding resin were less toxic than post-cured and removed unreacted layer samples of composite resin. Removal of the oxygen-inhibition layer resulted in the lowest cytotoxicity. Clinicians should remove unreacted monomers on the resin surface immediately after restoring teeth with light-curing resin to improve the restoration biocompatibility. PMID:28772647

  17. GROUND WATER SAMPLING USING LOW-FLOW TECHNIQUES

    EPA Science Inventory

    Obtaining representative ground water samples is important for site assessment and remedial performance monitoring objectives. The sampling device or method used to collect samples from monitoring or compliance well can significantly impact data quality and reliability. Low-flo...

  18. Effects of Heterogeneities, Sampling Frequencies, Tools and Methods on Uncertainties in Subsurface Contaminant Concentration Measurements

    NASA Astrophysics Data System (ADS)

    Ezzedine, S. M.; McNab, W. W.

    2007-12-01

    Long-term monitoring (LTM) is particularly important for contaminants which are mitigated by natural processes of dilution, dispersion, and degradation. At many sites, LTM can require decades of expensive sampling at tens or even hundreds of existing monitoring wells, resulting in hundreds of thousands, or millions of dollars per year for sampling and data management. Therefore, contaminant sampling tools, methods and frequencies are chosen to minimize waste and data management costs while ensuring a reliable and informative time-history of contaminant measurement for regulatory compliance. The interplay play between cause (i.e. subsurface heterogeneities, sampling techniques, measurement frequencies) and effect (unreliable data and measurements gap) has been overlooked in many field applications which can lead to inconsistencies in time- histories of contaminant samples. In this study we address the relationship between cause and effect for different hydrogeological sampling settings: porous and fractured media. A numerical model has been developed using AMR-FEM to solve the physicochemical processes that take place in the aquifer and the monitoring well. In the latter, the flow is governed by the Navier-Stokes equations while in the former the flow is governed by the diffusivity equation; both are fully coupled to mimic stressed conditions and to assess the effect of dynamic sampling tool on the formation surrounding the monitoring well. First of all, different sampling tools (i.e., Easy Pump, Snapper Grab Sampler) were simulated in a monitoring well screened in different homogeneous layered aquifers to assess their effect on the sampling measurements. Secondly, in order to make the computer runs more CPU efficient the flow in the monitoring well was replaced by its counterpart flow in porous media with infinite permeability and the new model was used to simulate the effect of heterogeneities, sampling depth, sampling tool and sampling frequencies on the

  19. Validation of a standardized extraction method for formalin-fixed paraffin-embedded tissue samples.

    PubMed

    Lagheden, Camilla; Eklund, Carina; Kleppe, Sara Nordqvist; Unger, Elizabeth R; Dillner, Joakim; Sundström, Karin

    2016-07-01

    Formalin-fixed paraffin-embedded (FFPE) samples can be DNA-extracted and used for human papillomavirus (HPV) genotyping. The xylene-based gold standard for extracting FFPE samples is laborious, suboptimal and involves health hazards for the personnel involved. To compare extraction with the standard xylene method to a xylene-free method used in an HPV LabNet Global Reference Laboratory at the Centers for Disease Control (CDC); based on a commercial method with an extra heating step. Fifty FFPE samples were randomly selected from a national audit of all cervical cancer cases diagnosed in Sweden during 10 years. For each case-block, a blank-block was sectioned, as a control for contamination. For xylene extraction, the standard WHO Laboratory Manual protocol was used. For the CDC method, the manufacturers' protocol was followed except for an extra heating step, 120°C for 20min. Samples were extracted and tested in parallel with β-globin real-time PCR, HPV16 real-time PCR and HPV typing using modified general primers (MGP)-PCR and Luminex assays. For a valid result the blank-block had to be betaglobin-negative in all tests and the case-block positive for beta-globin. Overall, detection was improved with the heating method and the amount of HPV-positive samples increased from 70% to 86% (p=0.039). For all samples where HPV type concordance could be evaluated, there was 100% type concordance. A xylene-free and robust extraction method for HPV-DNA typing in FFPE material is currently in great demand. Our proposed standardized protocol appears to be generally useful. Copyright © 2016. Published by Elsevier B.V.

  20. Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution

    PubMed Central

    Ingala, Melissa R.; Simmons, Nancy B.; Wultsch, Claudia; Krampis, Konstantinos; Speer, Kelly A.; Perkins, Susan L.

    2018-01-01

    The gut microbiome is a community of host-associated symbiotic microbes that fulfills multiple key roles in host metabolism, immune function, and tissue development. Given the ability of the microbiome to impact host fitness, there is increasing interest in studying the microbiome of wild animals to better understand these communities in the context of host ecology and evolution. Human microbiome research protocols are well established, but wildlife microbiome research is still a developing field. Currently, there is no standardized set of best practices guiding the collection of microbiome samples from wildlife. Gut microflora are typically sampled either by fecal collection, rectal swabbing, or by destructively sampling the intestinal contents of the host animal. Studies rarely include more than one sampling technique and no comparison of these methods currently exists for a wild mammal. Although some studies have hypothesized that the fecal microbiome is a nested subset of the intestinal microbiome, this hypothesis has not been formally tested. To address these issues, we examined guano (feces) and distal intestinal mucosa from 19 species of free-ranging bats from Lamanai, Belize, using 16S rRNA amplicon sequencing to compare microbial communities across sample types. We found that the diversity and composition of intestine and guano samples differed substantially. In addition, we conclude that signatures of host evolution are retained by studying gut microbiomes based on mucosal tissue samples, but not fecal samples. Conversely, fecal samples retained more signal of host diet than intestinal samples. These results suggest that fecal and intestinal sampling methods are not interchangeable, and that these two microbiotas record different information about the host from which they are isolated. PMID:29765359

  1. Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution.

    PubMed

    Ingala, Melissa R; Simmons, Nancy B; Wultsch, Claudia; Krampis, Konstantinos; Speer, Kelly A; Perkins, Susan L

    2018-01-01

    The gut microbiome is a community of host-associated symbiotic microbes that fulfills multiple key roles in host metabolism, immune function, and tissue development. Given the ability of the microbiome to impact host fitness, there is increasing interest in studying the microbiome of wild animals to better understand these communities in the context of host ecology and evolution. Human microbiome research protocols are well established, but wildlife microbiome research is still a developing field. Currently, there is no standardized set of best practices guiding the collection of microbiome samples from wildlife. Gut microflora are typically sampled either by fecal collection, rectal swabbing, or by destructively sampling the intestinal contents of the host animal. Studies rarely include more than one sampling technique and no comparison of these methods currently exists for a wild mammal. Although some studies have hypothesized that the fecal microbiome is a nested subset of the intestinal microbiome, this hypothesis has not been formally tested. To address these issues, we examined guano (feces) and distal intestinal mucosa from 19 species of free-ranging bats from Lamanai, Belize, using 16S rRNA amplicon sequencing to compare microbial communities across sample types. We found that the diversity and composition of intestine and guano samples differed substantially. In addition, we conclude that signatures of host evolution are retained by studying gut microbiomes based on mucosal tissue samples, but not fecal samples. Conversely, fecal samples retained more signal of host diet than intestinal samples. These results suggest that fecal and intestinal sampling methods are not interchangeable, and that these two microbiotas record different information about the host from which they are isolated.

  2. Quantifying responses of dung beetles to fire disturbance in tropical forests: the importance of trapping method and seasonality.

    PubMed

    de Andrade, Rafael Barreto; Barlow, Jos; Louzada, Julio; Vaz-de-Mello, Fernando Zagury; Souza, Mateus; Silveira, Juliana M; Cochrane, Mark A

    2011-01-01

    Understanding how biodiversity responds to environmental changes is essential to provide the evidence-base that underpins conservation initiatives. The present study provides a standardized comparison between unbaited flight intercept traps (FIT) and baited pitfall traps (BPT) for sampling dung beetles. We examine the effectiveness of the two to assess fire disturbance effects and how trap performance is affected by seasonality. The study was carried out in a transitional forest between Cerrado (Brazilian Savanna) and Amazon Forest. Dung beetles were collected during one wet and one dry sampling season. The two methods sampled different portions of the local beetle assemblage. Both FIT and BPT were sensitive to fire disturbance during the wet season, but only BPT detected community differences during the dry season. Both traps showed similar correlation with environmental factors. Our results indicate that seasonality had a stronger effect than trap type, with BPT more effective and robust under low population numbers, and FIT more sensitive to fine scale heterogeneity patterns. This study shows the strengths and weaknesses of two commonly used methodologies for sampling dung beetles in tropical forests, as well as highlighting the importance of seasonality in shaping the results obtained by both sampling strategies.

  3. Quantifying Responses of Dung Beetles to Fire Disturbance in Tropical Forests: The Importance of Trapping Method and Seasonality

    PubMed Central

    de Andrade, Rafael Barreto; Barlow, Jos; Louzada, Julio; Vaz-de-Mello, Fernando Zagury; Souza, Mateus; Silveira, Juliana M.; Cochrane, Mark A.

    2011-01-01

    Understanding how biodiversity responds to environmental changes is essential to provide the evidence-base that underpins conservation initiatives. The present study provides a standardized comparison between unbaited flight intercept traps (FIT) and baited pitfall traps (BPT) for sampling dung beetles. We examine the effectiveness of the two to assess fire disturbance effects and how trap performance is affected by seasonality. The study was carried out in a transitional forest between Cerrado (Brazilian Savanna) and Amazon Forest. Dung beetles were collected during one wet and one dry sampling season. The two methods sampled different portions of the local beetle assemblage. Both FIT and BPT were sensitive to fire disturbance during the wet season, but only BPT detected community differences during the dry season. Both traps showed similar correlation with environmental factors. Our results indicate that seasonality had a stronger effect than trap type, with BPT more effective and robust under low population numbers, and FIT more sensitive to fine scale heterogeneity patterns. This study shows the strengths and weaknesses of two commonly used methodologies for sampling dung beetles in tropical forests, as well as highlighting the importance of seasonality in shaping the results obtained by both sampling strategies. PMID:22028831

  4. Sample Size Methods for Estimating HIV Incidence from Cross-Sectional Surveys

    PubMed Central

    Brookmeyer, Ron

    2015-01-01

    Summary Understanding HIV incidence, the rate at which new infections occur in populations, is critical for tracking and surveillance of the epidemic. In this paper we derive methods for determining sample sizes for cross-sectional surveys to estimate incidence with sufficient precision. We further show how to specify sample sizes for two successive cross-sectional surveys to detect changes in incidence with adequate power. In these surveys biomarkers such as CD4 cell count, viral load, and recently developed serological assays are used to determine which individuals are in an early disease stage of infection. The total number of individuals in this stage, divided by the number of people who are uninfected, is used to approximate the incidence rate. Our methods account for uncertainty in the durations of time spent in the biomarker defined early disease stage. We find that failure to account for this uncertainty when designing surveys can lead to imprecise estimates of incidence and underpowered studies. We evaluated our sample size methods in simulations and found that they performed well in a variety of underlying epidemics. Code for implementing our methods in R is available with this paper at the Biometrics website on Wiley Online Library. PMID:26302040

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

    PubMed Central

    Marinelli, Fabrizio; Faraldo-Gómez, José D.

    2015-01-01

    We introduce an enhanced-sampling method for molecular dynamics (MD) simulations referred to as ensemble-biased metadynamics (EBMetaD). The method biases a conventional MD simulation to sample a molecular ensemble that is consistent with one or more probability distributions known a priori, e.g., experimental intramolecular distance distributions obtained by double electron-electron resonance or other spectroscopic techniques. To this end, EBMetaD adds an adaptive biasing potential throughout the simulation that discourages sampling of configurations inconsistent with the target probability distributions. The bias introduced is the minimum necessary to fulfill the target distributions, i.e., EBMetaD satisfies the maximum-entropy principle. Unlike other methods, EBMetaD does not require multiple simulation replicas or the introduction of Lagrange multipliers, and is therefore computationally efficient and straightforward in practice. We demonstrate the performance and accuracy of the method for a model system as well as for spin-labeled T4 lysozyme in explicit water, and show how EBMetaD reproduces three double electron-electron resonance distance distributions concurrently within a few tens of nanoseconds of simulation time. EBMetaD is integrated in the open-source PLUMED plug-in (www.plumed-code.org), and can be therefore readily used with multiple MD engines. PMID:26083917

  6. Sample size methods for estimating HIV incidence from cross-sectional surveys.

    PubMed

    Konikoff, Jacob; Brookmeyer, Ron

    2015-12-01

    Understanding HIV incidence, the rate at which new infections occur in populations, is critical for tracking and surveillance of the epidemic. In this article, we derive methods for determining sample sizes for cross-sectional surveys to estimate incidence with sufficient precision. We further show how to specify sample sizes for two successive cross-sectional surveys to detect changes in incidence with adequate power. In these surveys biomarkers such as CD4 cell count, viral load, and recently developed serological assays are used to determine which individuals are in an early disease stage of infection. The total number of individuals in this stage, divided by the number of people who are uninfected, is used to approximate the incidence rate. Our methods account for uncertainty in the durations of time spent in the biomarker defined early disease stage. We find that failure to account for this uncertainty when designing surveys can lead to imprecise estimates of incidence and underpowered studies. We evaluated our sample size methods in simulations and found that they performed well in a variety of underlying epidemics. Code for implementing our methods in R is available with this article at the Biometrics website on Wiley Online Library. © 2015, The International Biometric Society.

  7. An antithetic variate to facilitate upper-stem height measurements for critical height sampling with importance sampling

    Treesearch

    Thomas B. Lynch; Jeffrey H. Gove

    2013-01-01

    Critical height sampling (CHS) estimates cubic volume per unit area by multiplying the sum of critical heights measured on trees tallied in a horizontal point sample (HPS) by the HPS basal area factor. One of the barriers to practical application of CHS is the fact that trees near the field location of the point-sampling sample point have critical heights that occur...

  8. Testing common stream sampling methods for broad-scale, long-term monitoring

    Treesearch

    Eric K. Archer; Brett B. Roper; Richard C. Henderson; Nick Bouwes; S. Chad Mellison; Jeffrey L. Kershner

    2004-01-01

    We evaluated sampling variability of stream habitat sampling methods used by the USDA Forest Service and the USDI Bureau of Land Management monitoring program for the upper Columbia River Basin. Three separate studies were conducted to describe the variability of individual measurement techniques, variability between crews, and temporal variation throughout the summer...

  9. Sampling naturally contaminated broiler carcasses for Salmonella by three different methods

    USDA-ARS?s Scientific Manuscript database

    Postchill neck skin (NS) maceration and whole carcass rinsing (WCR) are frequently used methods to detect salmonellae from commercially processed broilers. These are practical, nondestructive methods, but they are insensitive and may result in frequent false negatives (20 to 40%). NS samples only ...

  10. Rapid-viability PCR method for detection of live, virulent Bacillus anthracis in environmental samples.

    PubMed

    Létant, Sonia E; Murphy, Gloria A; Alfaro, Teneile M; Avila, Julie R; Kane, Staci R; Raber, Ellen; Bunt, Thomas M; Shah, Sanjiv R

    2011-09-01

    In the event of a biothreat agent release, hundreds of samples would need to be rapidly processed to characterize the extent of contamination and determine the efficacy of remediation activities. Current biological agent identification and viability determination methods are both labor- and time-intensive such that turnaround time for confirmed results is typically several days. In order to alleviate this issue, automated, high-throughput sample processing methods were developed in which real-time PCR analysis is conducted on samples before and after incubation. The method, referred to as rapid-viability (RV)-PCR, uses the change in cycle threshold after incubation to detect the presence of live organisms. In this article, we report a novel RV-PCR method for detection of live, virulent Bacillus anthracis, in which the incubation time was reduced from 14 h to 9 h, bringing the total turnaround time for results below 15 h. The method incorporates a magnetic bead-based DNA extraction and purification step prior to PCR analysis, as well as specific real-time PCR assays for the B. anthracis chromosome and pXO1 and pXO2 plasmids. A single laboratory verification of the optimized method applied to the detection of virulent B. anthracis in environmental samples was conducted and showed a detection level of 10 to 99 CFU/sample with both manual and automated RV-PCR methods in the presence of various challenges. Experiments exploring the relationship between the incubation time and the limit of detection suggest that the method could be further shortened by an additional 2 to 3 h for relatively clean samples.

  11. Sample preparation method influences direct identification of anaerobic bacteria from positive blood culture bottles using MALDI-TOF MS.

    PubMed

    Jeverica, Samo; Nagy, Elisabeth; Mueller-Premru, Manica; Papst, Lea

    2018-05-15

    Rapid detection and identification of anaerobic bacteria from blood is important to adjust antimicrobial therapy by including antibiotics with activity against anaerobic bacteria. Limited data is available about direct identification of anaerobes from positive blood culture bottles using MALDI-TOF mass spectrometry (MS). In this study, we evaluated the performance of two sample preparation protocols for direct identification of anaerobes from positive blood culture bottles, the MALDI Sepsityper kit (Sepsityper) and the in-house saponin (saponin) method. Additionally, we compared two blood culture bottle types designed to support the growth of anaerobic bacteria, the BacT/ALERT-FN Plus (FN Plus) and the BACTEC-Lytic (Lytic), and their influence on direct identification. A selection of 30 anaerobe strains belonging to 22 different anaerobic species (11 reference strains and 19 clinical isolates) were inoculated to 2 blood culture bottle types in duplicate. In total, 120 bottles were inoculated and 99.2% (n = 119) signalled growth within 5 days of incubation. The Sepsityper method correctly identified 56.3% (n = 67) of anaerobes, while the saponin method correctly identified 84.9% (n = 101) of anaerobes with at least log(score) ≥1.6 (low confidence correct identification), (p < 0.001). Gram negative anaerobes were better identified with the saponin method (100% vs. 46.5%; p < 0.001), while Gram positive anaerobes were better identified with the Sepsityper method (70.8% vs. 62.5%; p = 0.454). Average log(score) values among only those isolates that were correctly identified simultaneously by both sample preparation methods were 2.119 and 2.029 in favour of the Sepsityper method, (p = 0.019). The inoculated bottle type didn't influence the performance of the two sample preparation methods. We confirmed that direct identification from positive blood culture bottles with MALDI-TOF MS is reliable for anaerobic bacteria. However, the results

  12. Comparison of three methods of sampling trout blood for measurements of hematocrit

    USGS Publications Warehouse

    Steucke, Erwin W.; Schoettger, Richard A.

    1967-01-01

    Trout blood is frequently collected for hematocrit measurements by excising the caudal fin (Snieszko, 1960), but this technique is impractical if valuable fish are to be sampled or if repeated observations are desired. Schiffman (1959) and Snieszko (1960) collected blood from the dorsal aorta and the heart, but these methods are relatively slow and require the preparation of needles and syringes. The use of pointed capillary tubes for cardiac punctures increases the speed of sampling, but body fluids may dilute the blood (Perkins, 1957; Larsen and Snieszko, 1961; and Normandau, 1962). There is need for methods of sampling which are rapid and which neither influence hematological determinations nor harm the fish.

  13. Nonuniform sampling and non-Fourier signal processing methods in multidimensional NMR.

    PubMed

    Mobli, Mehdi; Hoch, Jeffrey C

    2014-11-01

    Beginning with the introduction of Fourier Transform NMR by Ernst and Anderson in 1966, time domain measurement of the impulse response (the free induction decay, FID) consisted of sampling the signal at a series of discrete intervals. For compatibility with the discrete Fourier transform (DFT), the intervals are kept uniform, and the Nyquist theorem dictates the largest value of the interval sufficient to avoid aliasing. With the proposal by Jeener of parametric sampling along an indirect time dimension, extension to multidimensional experiments employed the same sampling techniques used in one dimension, similarly subject to the Nyquist condition and suitable for processing via the discrete Fourier transform. The challenges of obtaining high-resolution spectral estimates from short data records using the DFT were already well understood, however. Despite techniques such as linear prediction extrapolation, the achievable resolution in the indirect dimensions is limited by practical constraints on measuring time. The advent of non-Fourier methods of spectrum analysis capable of processing nonuniformly sampled data has led to an explosion in the development of novel sampling strategies that avoid the limits on resolution and measurement time imposed by uniform sampling. The first part of this review discusses the many approaches to data sampling in multidimensional NMR, the second part highlights commonly used methods for signal processing of such data, and the review concludes with a discussion of other approaches to speeding up data acquisition in NMR. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. Nonuniform sampling and non-Fourier signal processing methods in multidimensional NMR

    PubMed Central

    Mobli, Mehdi; Hoch, Jeffrey C.

    2017-01-01

    Beginning with the introduction of Fourier Transform NMR by Ernst and Anderson in 1966, time domain measurement of the impulse response (the free induction decay, FID) consisted of sampling the signal at a series of discrete intervals. For compatibility with the discrete Fourier transform (DFT), the intervals are kept uniform, and the Nyquist theorem dictates the largest value of the interval sufficient to avoid aliasing. With the proposal by Jeener of parametric sampling along an indirect time dimension, extension to multidimensional experiments employed the same sampling techniques used in one dimension, similarly subject to the Nyquist condition and suitable for processing via the discrete Fourier transform. The challenges of obtaining high-resolution spectral estimates from short data records using the DFT were already well understood, however. Despite techniques such as linear prediction extrapolation, the achievable resolution in the indirect dimensions is limited by practical constraints on measuring time. The advent of non-Fourier methods of spectrum analysis capable of processing nonuniformly sampled data has led to an explosion in the development of novel sampling strategies that avoid the limits on resolution and measurement time imposed by uniform sampling. The first part of this review discusses the many approaches to data sampling in multidimensional NMR, the second part highlights commonly used methods for signal processing of such data, and the review concludes with a discussion of other approaches to speeding up data acquisition in NMR. PMID:25456315

  15. Investigation of solvent-free MALDI-TOFMS sample preparation methods for the analysis of organometallic and coordination compounds.

    PubMed

    Hughes, Laura; Wyatt, Mark F; Stein, Bridget K; Brenton, A Gareth

    2009-01-15

    An investigation of various solvent-free matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) sample preparation methods for the characterization of organometallic and coordination compounds is described. Such methods are desirable for insoluble materials, compounds that are only soluble in disadvantageous solvents, or complexes that dissociate in solution, all of which present a major "difficulty" to most mass spectrometry techniques. First-row transition metal acetylacetonate complexes, which have been characterized previously by solution preparation MALDI-TOFMS, were used to evaluate the various solvent-free procedures. These procedures comprise two distinct steps: the first being the efficient "solids mixing" (the mixing of sample and matrix), and the second being the effective transfer of the sample/matrix mixture to the MALDI target plate. This investigation shows that vortex mixing is the most efficient first step and that smearing using a microspatula is the most effective second step. In addition, the second step is shown to be much more critical than the first step in obtaining high-quality data. Case studies of truly insoluble materials highlight the importance of these techniques for the wider chemistry community.

  16. A study of method robustness for arsenic speciation in drinking water samples by anion exchange HPLC-ICP-MS.

    PubMed

    Day, Jason A; Montes-Bayón, María; Vonderheide, Anne P; Caruso, Joseph A

    2002-08-01

    Regulating arsenic species in drinking waters is a reasonable objective, since the various species have different toxicological impacts. However, developing robust and sensitive speciation methods is mandatory prior to any such regulations. Numerous arsenic speciation publications exist, but the question of robustness or ruggedness for a regulatory method has not been fully explored. The present work illustrates the use of anion exchange chromatography coupled to ICP-MS with a commercially available "speciation kit" option. The mobile phase containing 2 mM NaH(2)PO(4) and 0.2 mM EDTA at pH 6 allowed adequate separation of four As species (As(III), As(V), MMAA, DMAA) in less than 10 min. The analytical performance characteristics studied, including method detection limits (lower than 100 ng L(-1) for all the species evaluated), proved the suitability of the method to fulfill the current regulation. Other parameters evaluated such as laboratory fortified blanks, spiked recoveries, and reproducibility over a certain period of time produced adequate results. The samples analyzed were taken from water utilities in different areas of the United States and were provided by the U.S. EPA. The data suggests the speciation setup performs to U.S. EPA specifications but sample treatment and chemistry are also important factors for achieving good recoveries for samples spiked with As(III) as arsenite and As(V) as arsenate.

  17. A General Linear Method for Equating with Small Samples

    ERIC Educational Resources Information Center

    Albano, Anthony D.

    2015-01-01

    Research on equating with small samples has shown that methods with stronger assumptions and fewer statistical estimates can lead to decreased error in the estimated equating function. This article introduces a new approach to linear observed-score equating, one which provides flexible control over how form difficulty is assumed versus estimated…

  18. Cryptosporidium Oocyst Detection in Water Samples: Floatation Technique Enhanced with Immunofluorescence Is as Effective as Immunomagnetic Separation Method

    PubMed Central

    Koompapong, Khuanchai; Sutthikornchai, Chantira

    2009-01-01

    Cryptosporidium can cause gastrointestinal diseases worldwide, consequently posing public health problems and economic burden. Effective techniques for detecting contaminated oocysts in water are important to prevent and control the contamination. Immunomagnetic separation (IMS) method has been widely employed recently due to its efficiency, but, it is costly. Sucrose floatation technique is generally used for separating organisms by using their different specific gravity. It is effective and cheap but time consuming as well as requiring highly skilled personnel. Water turbidity and parasite load in water sample are additional factors affecting to the recovery rate of those 2 methods. We compared the efficiency of IMS and sucrose floatation methods to recover the spiked Cryptosporidium oocysts in various turbidity water samples. Cryptosporidium oocysts concentration at 1, 101, 102, and 103 per 10 µl were spiked into 3 sets of 10 ml-water turbidity (5, 50, and 500 NTU). The recovery rate of the 2 methods was not different. Oocyst load at the concentration < 102 per 10 ml yielded unreliable results. Water turbidity at 500 NTU decreased the recovery rate of both techniques. The combination of sucrose floatation and immunofluorescense assay techniques (SF-FA) showed higher recovery rate than IMS and immunofluorescense assay (IMS-FA). We used this SF-FA to detect Cryptosporidium and Giardia from the river water samples and found 9 and 19 out of 30 (30% and 63.3%) positive, respectively. Our results favored sucrose floatation technique enhanced with immunofluorescense assay for detecting contaminated protozoa in water samples in general laboratories and in the real practical setting. PMID:19967082

  19. Cryptosporidium oocyst detection in water samples: floatation technique enhanced with immunofluorescence is as effective as immunomagnetic separation method.

    PubMed

    Koompapong, Khuanchai; Sutthikornchai, Chantira; Sukthana, Yowalark

    2009-12-01

    Cryptosporidium can cause gastrointestinal diseases worldwide, consequently posing public health problems and economic burden. Effective techniques for detecting contaminated oocysts in water are important to prevent and control the contamination. Immunomagnetic separation (IMS) method has been widely employed recently due to its efficiency, but, it is costly. Sucrose floatation technique is generally used for separating organisms by using their different specific gravity. It is effective and cheap but time consuming as well as requiring highly skilled personnel. Water turbidity and parasite load in water sample are additional factors affecting to the recovery rate of those 2 methods. We compared the efficiency of IMS and sucrose floatation methods to recover the spiked Cryptosporidium oocysts in various turbidity water samples. Cryptosporidium oocysts concentration at 1, 10(1), 10(2), and 10(3) per 10 microl were spiked into 3 sets of 10 ml-water turbidity (5, 50, and 500 NTU). The recovery rate of the 2 methods was not different. Oocyst load at the concentration < 10(2) per 10 ml yielded unreliable results. Water turbidity at 500 NTU decreased the recovery rate of both techniques. The combination of sucrose floatation and immunofluorescense assay techniques (SF-FA) showed higher recovery rate than IMS and immunofluorescense assay (IMS-FA). We used this SF-FA to detect Cryptosporidium and Giardia from the river water samples and found 9 and 19 out of 30 (30% and 63.3%) positive, respectively. Our results favored sucrose floatation technique enhanced with immunofluorescense assay for detecting contaminated protozoa in water samples in general laboratories and in the real practical setting.

  20. Sampling methods for recovery of human enteric viruses from environmental surfaces.

    PubMed

    Turnage, Nicole L; Gibson, Kristen E

    2017-10-01

    Acute gastroenteritis causes the second highest infectious disease burden worldwide. Human enteric viruses have been identified as leading causative agents of acute gastroenteritis as well as foodborne illnesses in the U.S. and are generally transmitted by fecal-oral contamination. There is growing evidence of transmission occurring via contaminated fomite including food contact surfaces. Additionally, human enteric viruses have been shown to remain infectious on fomites over prolonged periods of time. To better understand viral persistence, there is a need for more studies to investigate this phenomenon. Therefore, optimization of surface sampling methods is essential to aid in understanding environmental contamination to ensure proper preventative measures are being applied. In general, surface sampling studies are limited and highly variable among recovery efficiencies and research parameters used (e.g., virus type/density, surface type, elution buffers, tools). This review aims to discuss the various factors impacting surface sampling of viruses from fomites and to explore how researchers could move towards a more sensitive and standard sampling method. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Comparing respondent-driven sampling and targeted sampling methods of recruiting injection drug users in San Francisco.

    PubMed

    Kral, Alex H; Malekinejad, Mohsen; Vaudrey, Jason; Martinez, Alexis N; Lorvick, Jennifer; McFarland, Willi; Raymond, H Fisher

    2010-09-01

    The objective of this article is to compare demographic characteristics, risk behaviors, and service utilization among injection drug users (IDUs) recruited from two separate studies in San Francisco in 2005, one which used targeted sampling (TS) and the other which used respondent-driven sampling (RDS). IDUs were recruited using TS (n = 651) and RDS (n = 534) and participated in quantitative interviews that included demographic characteristics, risk behaviors, and service utilization. Prevalence estimates and 95% confidence intervals (CIs) were calculated to assess whether there were differences in these variables by sampling method. There was overlap in 95% CIs for all demographic variables except African American race (TS: 45%, 53%; RDS: 29%, 44%). Maps showed that the proportion of IDUs distributed across zip codes were similar for the TS and RDS sample, with the exception of a single zip code that was more represented in the TS sample. This zip code includes an isolated, predominantly African American neighborhood where only the TS study had a field site. Risk behavior estimates were similar for both TS and RDS samples, although self-reported hepatitis C infection was lower in the RDS sample. In terms of service utilization, more IDUs in the RDS sample reported no recent use of drug treatment and syringe exchange program services. Our study suggests that perhaps a hybrid sampling plan is best suited for recruiting IDUs in San Francisco, whereby the more intensive ethnographic and secondary analysis components of TS would aid in the planning of seed placement and field locations for RDS.

  2. Recommendations for level-determined sampling in wells

    NASA Astrophysics Data System (ADS)

    Lerner, David N.; Teutsch, Georg

    1995-10-01

    Level-determined samples of groundwater are increasingly important for hydrogeological studies. The techniques for collecting them range from the use of purpose drilled wells, sometimes with sophisticated dedicated multi-level samplers in them, to a variety of methods used in open wells. Open, often existing, wells are frequently used on cost grounds, but there are risks of obtaining poor and unrepresentative samples. Alternative approaches to level-determined sampling incorporate seven concepts: depth sampling; packer systems; individual wells; dedicated multi-level systems; separation pumping; baffle systems; multi-port sock samplers. These are outlined and evaluated in terms of the environment to be sampled, and the features and performance of the methods. Recommendations are offered to match methods to sampling problems.

  3. Optical method for the characterization of laterally-patterned samples in integrated circuits

    DOEpatents

    Maris, Humphrey J.

    2001-01-01

    Disclosed is a method for characterizing a sample having a structure disposed on or within the sample, comprising the steps of applying a first pulse of light to a surface of the sample for creating a propagating strain pulse in the sample, applying a second pulse of light to the surface so that the second pulse of light interacts with the propagating strain pulse in the sample, sensing from a reflection of the second pulse a change in optical response of the sample, and relating a time of occurrence of the change in optical response to at least one dimension of the structure.

  4. Optical method for the characterization of laterally-patterned samples in integrated circuits

    DOEpatents

    Maris, Humphrey J.

    2010-08-24

    Disclosed is a method for characterizing a sample having a structure disposed on or within the sample, comprising the steps of applying a first pulse of light to a surface of the sample for creating a propagating strain pulse in the sample, applying a second pulse of light to the surface so that the second pulse of light interacts with the propagating strain pulse in the sample, sensing from a reflection of the second pulse a change in optical response of the sample, and relating a time of occurrence of the change in optical response to at least one dimension of the structure.

  5. Optical method for the characterization of laterally patterned samples in integrated circuits

    DOEpatents

    Maris, Humphrey J [Barrington, RI

    2009-03-17

    Disclosed is a method for characterizing a sample having a structure disposed on or within the sample, comprising the steps of applying a first pulse of light to a surface of the sample for creating a propagating strain pulse in the sample, applying a second pulse of light to the surface so that the second pulse of light interacts with the propagating strain pulse in the sample, sensing from a reflection of the second pulse a change in optical response of the sample, and relating a time of occurrence of the change in optical response to at least one dimension of the structure.

  6. Importance of tissue sampling, laboratory methods, and patient characteristics for detection of Pneumocystis in autopsied lungs of non-immunosuppressed individuals.

    PubMed

    Vargas, S L; Ponce, C; Bustamante, R; Calderón, E; Nevez, G; De Armas, Y; Matos, O; Miller, R F; Gallo, M J

    2017-10-01

    To understand the epidemiological significance of Pneumocystis detection in a lung tissue sample of non-immunosuppressed individuals, we examined sampling procedures, laboratory methodology, and patient characteristics of autopsy series reported in the literature. Number of tissue specimens, DNA-extraction procedures, age and underlying diagnosis highly influence yield and are critical to understand yield differences of Pneumocystis among reports of pulmonary colonization in immunocompetent individuals.

  7. Acceleration of intensity-modulated radiotherapy dose calculation by importance sampling of the calculation matrices.

    PubMed

    Thieke, Christian; Nill, Simeon; Oelfke, Uwe; Bortfeld, Thomas

    2002-05-01

    In inverse planning for intensity-modulated radiotherapy, the dose calculation is a crucial element limiting both the maximum achievable plan quality and the speed of the optimization process. One way to integrate accurate dose calculation algorithms into inverse planning is to precalculate the dose contribution of each beam element to each voxel for unit fluence. These precalculated values are stored in a big dose calculation matrix. Then the dose calculation during the iterative optimization process consists merely of matrix look-up and multiplication with the actual fluence values. However, because the dose calculation matrix can become very large, this ansatz requires a lot of computer memory and is still very time consuming, making it not practical for clinical routine without further modifications. In this work we present a new method to significantly reduce the number of entries in the dose calculation matrix. The method utilizes the fact that a photon pencil beam has a rapid radial dose falloff, and has very small dose values for the most part. In this low-dose part of the pencil beam, the dose contribution to a voxel is only integrated into the dose calculation matrix with a certain probability. Normalization with the reciprocal of this probability preserves the total energy, even though many matrix elements are omitted. Three probability distributions were tested to find the most accurate one for a given memory size. The sampling method is compared with the use of a fully filled matrix and with the well-known method of just cutting off the pencil beam at a certain lateral distance. A clinical example of a head and neck case is presented. It turns out that a sampled dose calculation matrix with only 1/3 of the entries of the fully filled matrix does not sacrifice the quality of the resulting plans, whereby the cutoff method results in a suboptimal treatment plan.

  8. Biofouling development on plasma treated samples versus layers coated samples

    NASA Astrophysics Data System (ADS)

    Hnatiuc, B.; Exnar, P.; Sabau, A.; Spatenka, P.; Dumitrache, C. L.; Hnatiuc, M.; Ghita, S.

    2016-12-01

    Biofouling is the most important cause of naval corrosion. In order to reduce the Biofouling development on naval materials as steel or resin, different new methods have been tested. These methods could help to follow the new IMO environment reglementations and they could replace few classic operations before the painting of the small ships. The replacement of these operations means a reduction in maintenance costs. Their action must influence especially the first two steps of the Biofouling development, called Microfouling, that demand about 24 hours. This work presents the comparative results of the Biofouling development on two different classic naval materials, steel and resin, for three treated samples, immersed in sea water. Non-thermal plasma, produced by GlidArc technology, is applied to the first sample, called GD. The plasma treatment was set to 10 minutes. The last two samples, called AE9 and AE10 are covered by hydrophobic layers, prepared from a special organic-inorganic sol synthesized by sol-gel method. Theoretically, because of the hydrophobic properties, the Biofouling formation must be delayed for AE9 and AE10. The Biofouling development on each treated sample was compared with a witness non-treated sample. The microbiological analyses have been done for 24 hours by epifluorescence microscopy, available for one single layer.

  9. [Comparison study on sampling methods of Oncomelania hupensis snail survey in marshland schistosomiasis epidemic areas in China].

    PubMed

    An, Zhao; Wen-Xin, Zhang; Zhong, Yao; Yu-Kuan, Ma; Qing, Liu; Hou-Lang, Duan; Yi-di, Shang

    2016-06-29

    To optimize and simplify the survey method of Oncomelania hupensis snail in marshland endemic region of schistosomiasis and increase the precision, efficiency and economy of the snail survey. A quadrate experimental field was selected as the subject of 50 m×50 m size in Chayegang marshland near Henghu farm in the Poyang Lake region and a whole-covered method was adopted to survey the snails. The simple random sampling, systematic sampling and stratified random sampling methods were applied to calculate the minimum sample size, relative sampling error and absolute sampling error. The minimum sample sizes of the simple random sampling, systematic sampling and stratified random sampling methods were 300, 300 and 225, respectively. The relative sampling errors of three methods were all less than 15%. The absolute sampling errors were 0.221 7, 0.302 4 and 0.047 8, respectively. The spatial stratified sampling with altitude as the stratum variable is an efficient approach of lower cost and higher precision for the snail survey.

  10. Relative efficiency of anuran sampling methods in a restinga habitat (Jurubatiba, Rio de Janeiro, Brazil).

    PubMed

    Rocha, C F D; Van Sluys, M; Hatano, F H; Boquimpani-Freitas, L; Marra, R V; Marques, R V

    2004-11-01

    Studies on anurans in restinga habitats are few and, as a result, there is little information on which methods are more efficient for sampling them in this environment. Ten methods are usually used for sampling anuran communities in tropical and sub-tropical areas. In this study we evaluate which methods are more appropriate for this purpose in the restinga environment of Parque Nacional da Restinga de Jurubatiba. We analyzed six methods among those usually used for anuran samplings. For each method, we recorded the total amount of time spent (in min.), the number of researchers involved, and the number of species captured. We calculated a capture efficiency index (time necessary for a researcher to capture an individual frog) in order to make comparable the data obtained. Of the methods analyzed, the species inventory (9.7 min/searcher /ind.- MSI; richness = 6; abundance = 23) and the breeding site survey (9.5 MSI; richness = 4; abundance = 22) were the most efficient. The visual encounter inventory (45.0 MSI) and patch sampling (65.0 MSI) methods were of comparatively lower efficiency restinga, whereas the plot sampling and the pit-fall traps with drift-fence methods resulted in no frog capture. We conclude that there is a considerable difference in efficiency of methods used in the restinga environment and that the complete species inventory method is highly efficient for sampling frogs in the restinga studied and may be so in other restinga environments. Methods that are usually efficient in forested areas seem to be of little value in open restinga habitats.

  11. Quantitative method of determining beryllium or a compound thereof in a sample

    DOEpatents

    McCleskey, T. Mark; Ehler, Deborah S.; John, Kevin D.; Burrell, Anthony K.; Collis, Gavin E.; Minogue, Edel M.; Warner, Benjamin P.

    2006-10-31

    A method of determining beryllium or a beryllium compound thereof in a sample, includes providing a sample suspected of comprising beryllium or a compound thereof, extracting beryllium or a compound thereof from the sample by dissolving in a solution, adding a fluorescent indicator to the solution to thereby bind any beryllium or a compound thereof to the fluorescent indicator, and determining the presence or amount of any beryllium or a compound thereof in the sample by measuring fluorescence.

  12. Quantitative method of determining beryllium or a compound thereof in a sample

    DOEpatents

    McCleskey, T. Mark; Ehler, Deborah S.; John, Kevin D.; Burrell, Anthony K.; Collis, Gavin E.; Minogue, Edel M.; Warner, Benjamin P.

    2010-08-24

    A method of determining beryllium or a beryllium compound thereof in a sample, includes providing a sample suspected of comprising beryllium or a compound thereof, extracting beryllium or a compound thereof from the sample by dissolving in a solution, adding a fluorescent indicator to the solution to thereby bind any beryllium or a compound thereof to the fluorescent indicator, and determining the presence or amount of any beryllium or a compound thereof in the sample by measuring fluorescence.

  13. Electrodeposition as an alternate method for preparation of environmental samples for iodide by AMS

    DOE PAGES

    Adamic, M. L.; Lister, T. E.; Dufek, E. J.; ...

    2015-03-25

    This paper presents an evaluation of an alternate method for preparing environmental samples for 129I analysis by accelerator mass spectrometry (AMS) at Idaho National Laboratory. The optimal sample preparation method is characterized by ease of preparation, capability of processing very small quantities of iodide, and ease of loading into a cathode. Electrodeposition of iodide on a silver wire was evaluated using these criteria. This study indicates that the electrochemically-formed silver iodide deposits produce ion currents similar to those from precipitated silver iodide for the same sample mass. Furthermore, precipitated silver iodide samples are usually mixed with niobium or silver powdermore » prior to loading in a cathode. Using electrodeposition, the silver is already mixed with the sample and can simply be picked up with tweezers, placed in the sample die, and pressed into a cathode. The major advantage of this method is that the silver wire/electrodeposited silver iodide is much easier to load into a cathode.« less

  14. Fast acquisition of multidimensional NMR spectra of solids and mesophases using alternative sampling methods.

    PubMed

    Lesot, Philippe; Kazimierczuk, Krzysztof; Trébosc, Julien; Amoureux, Jean-Paul; Lafon, Olivier

    2015-11-01

    Unique information about the atom-level structure and dynamics of solids and mesophases can be obtained by the use of multidimensional nuclear magnetic resonance (NMR) experiments. Nevertheless, the acquisition of these experiments often requires long acquisition times. We review here alternative sampling methods, which have been proposed to circumvent this issue in the case of solids and mesophases. Compared to the spectra of solutions, those of solids and mesophases present some specificities because they usually display lower signal-to-noise ratios, non-Lorentzian line shapes, lower spectral resolutions and wider spectral widths. We highlight herein the advantages and limitations of these alternative sampling methods. A first route to accelerate the acquisition time of multidimensional NMR spectra consists in the use of sparse sampling schemes, such as truncated, radial or random sampling ones. These sparsely sampled datasets are generally processed by reconstruction methods differing from the Discrete Fourier Transform (DFT). A host of non-DFT methods have been applied for solids and mesophases, including the G-matrix Fourier transform, the linear least-square procedures, the covariance transform, the maximum entropy and the compressed sensing. A second class of alternative sampling consists in departing from the Jeener paradigm for multidimensional NMR experiments. These non-Jeener methods include Hadamard spectroscopy as well as spatial or orientational encoding of the evolution frequencies. The increasing number of high field NMR magnets and the development of techniques to enhance NMR sensitivity will contribute to widen the use of these alternative sampling methods for the study of solids and mesophases in the coming years. Copyright © 2015 John Wiley & Sons, Ltd.

  15. Sequential sampling: a novel method in farm animal welfare assessment.

    PubMed

    Heath, C A E; Main, D C J; Mullan, S; Haskell, M J; Browne, W J

    2016-02-01

    Lameness in dairy cows is an important welfare issue. As part of a welfare assessment, herd level lameness prevalence can be estimated from scoring a sample of animals, where higher levels of accuracy are associated with larger sample sizes. As the financial cost is related to the number of cows sampled, smaller samples are preferred. Sequential sampling schemes have been used for informing decision making in clinical trials. Sequential sampling involves taking samples in stages, where sampling can stop early depending on the estimated lameness prevalence. When welfare assessment is used for a pass/fail decision, a similar approach could be applied to reduce the overall sample size. The sampling schemes proposed here apply the principles of sequential sampling within a diagnostic testing framework. This study develops three sequential sampling schemes of increasing complexity to classify 80 fully assessed UK dairy farms, each with known lameness prevalence. Using the Welfare Quality herd-size-based sampling scheme, the first 'basic' scheme involves two sampling events. At the first sampling event half the Welfare Quality sample size is drawn, and then depending on the outcome, sampling either stops or is continued and the same number of animals is sampled again. In the second 'cautious' scheme, an adaptation is made to ensure that correctly classifying a farm as 'bad' is done with greater certainty. The third scheme is the only scheme to go beyond lameness as a binary measure and investigates the potential for increasing accuracy by incorporating the number of severely lame cows into the decision. The three schemes are evaluated with respect to accuracy and average sample size by running 100 000 simulations for each scheme, and a comparison is made with the fixed size Welfare Quality herd-size-based sampling scheme. All three schemes performed almost as well as the fixed size scheme but with much smaller average sample sizes. For the third scheme, an overall

  16. THE INFLUENCE OF PHYSICAL FACTORS ON COMPARATIVE PERFORMANCE OF SAMPLING METHODS IN LARGE RIVERS

    EPA Science Inventory

    In 1999, we compared five existing benthic macroinvertebrate sampling methods used in boatable rivers. Each sampling protocol was performed at each of 60 sites distributed among four rivers in the Ohio River drainage basin. Initial comparison of methods using key macroinvertebr...

  17. Laser based water equilibration method for d18O determination of water samples

    NASA Astrophysics Data System (ADS)

    Mandic, Magda; Smajgl, Danijela; Stoebener, Nils

    2017-04-01

    Determination of d18O with water equilibration method using mass spectrometers equipped with equilibration unit or Gas Bench is known already for many years. Now, with development of laser spectrometers this extends methods and possibilities to apply different technologies in laboratory but also in the field. The Thermo Scientific™ Delta Ray™ Isotope Ratio Infrared Spectrometer (IRIS) analyzer with the Universal Reference Interface (URI) Connect and Teledyne Cetac ASX-7100 offers high precision and throughput of samples. It employs optical spectroscopy for continuous measurement of isotope ratio values and concentration of carbon dioxide in ambient air, and also for analysis of discrete samples from vials, syringes, bags, or other user-provided sample containers. Test measurements and conformation of precision and accuracy of method determination d18O in water samples were done in Thermo Fisher application laboratory with three lab standards, namely ANST, Ocean II and HBW. All laboratory standards were previously calibrated with international reference material VSMOW2 and SLAP2 to assure accuracy of the isotopic values of the water. With method that we present in this work achieved repeatability and accuracy are 0.16‰ and 0.71‰, respectively, which fulfill requirements of regulatory method for wine and must after equilibration with CO2.

  18. Method of analyzing multiple sample simultaneously by detecting absorption and systems for use in such a method

    DOEpatents

    Yeung, Edward S.; Gong, Xiaoyi

    2004-09-07

    The present invention provides a method of analyzing multiple samples simultaneously by absorption detection. The method comprises: (i) providing a planar array of multiple containers, each of which contains a sample comprising at least one absorbing species, (ii) irradiating the planar array of multiple containers with a light source and (iii) detecting absorption of light with a detetion means that is in line with the light source at a distance of at leaat about 10 times a cross-sectional distance of a container in the planar array of multiple containers. The absorption of light by a sample indicates the presence of an absorbing species in it. The method can further comprise: (iv) measuring the amount of absorption of light detected in (iii) indicating the amount of the absorbing species in the sample. Also provided by the present invention is a system for use in the abov metho.The system comprises; (i) a light source comrnpising or consisting essentially of at leaat one wavelength of light, the absorption of which is to be detected, (ii) a planar array of multiple containers, and (iii) a detection means that is in line with the light source and is positioned in line with and parallel to the planar array of multiple contiainers at a distance of at least about 10 times a cross-sectional distance of a container.

  19. Materials and Methods for Streamlined Laboratory Analysis of Environmental Samples, FY 2016 Report

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Addleman, Raymond S.; Naes, Benjamin E.; McNamara, Bruce K.

    The International Atomic Energy Agency (IAEA) relies upon laboratory analysis of environmental samples (typically referred to as “swipes”) collected during on-site inspections of safeguarded facilities to support the detection and deterrence of undeclared activities. Unfortunately, chemical processing and assay of the samples is slow and expensive. A rapid, effective, and simple extraction process and analysis method is needed to provide certified results with improved timeliness at reduced costs (principally in the form of reduced labor), while maintaining or improving sensitivity and efficacy. To address these safeguard needs the Pacific Northwest National Laboratory (PNNL) explored and demonstrated improved methods for environmentalmore » sample (ES) analysis. Improvements for both bulk and particle analysis were explored. To facilitate continuity and adoption, the new sampling materials and processing methods will be compatible with existing IAEA protocols for ES analysis. PNNL collaborated with Oak Ridge National Laboratory (ORNL), which performed independent validation of the new bulk analysis methods and compared performance to traditional IAEA’s Network of Analytical Laboratories (NWAL) protocol. ORNL efforts are reported separately. This report describes PNNL’s FY 2016 progress, which was focused on analytical application supporting environmental monitoring of uranium enrichment plants and nuclear fuel processing. In the future the technology could be applied to other safeguard applications and analytes related to fuel manufacturing, reprocessing, etc. PNNL’s FY 2016 efforts were broken into two tasks and a summary of progress, accomplishments and highlights are provided below. Principal progress and accomplishments on Task 1, Optimize Materials and Methods for ICP-MS Environmental Sample Analysis, are listed below. • Completed initial procedure for rapid uranium extraction from ES swipes based upon carbonate-peroxide chemistry (delivered to

  20. Comparison of the acetyl bromide spectrophotometric method with other analytical lignin methods for determining lignin concentration in forage samples.

    PubMed

    Fukushima, Romualdo S; Hatfield, Ronald D

    2004-06-16

    Present analytical methods to quantify lignin in herbaceous plants are not totally satisfactory. A spectrophotometric method, acetyl bromide soluble lignin (ABSL), has been employed to determine lignin concentration in a range of plant materials. In this work, lignin extracted with acidic dioxane was used to develop standard curves and to calculate the derived linear regression equation (slope equals absorptivity value or extinction coefficient) for determining the lignin concentration of respective cell wall samples. This procedure yielded lignin values that were different from those obtained with Klason lignin, acid detergent acid insoluble lignin, or permanganate lignin procedures. Correlations with in vitro dry matter or cell wall digestibility of samples were highest with data from the spectrophotometric technique. The ABSL method employing as standard lignin extracted with acidic dioxane has the potential to be employed as an analytical method to determine lignin concentration in a range of forage materials. It may be useful in developing a quick and easy method to predict in vitro digestibility on the basis of the total lignin content of a sample.

  1. GROUND WATER MONITORING AND SAMPLING: MULTI-LEVEL VERSUS TRADITIONAL METHODS WHATS WHAT?

    EPA Science Inventory

    After years of research and many publications, the question still remains: What is the best method to collect representative ground water samples from monitoring wells? Numerous systems and devices are currently available for obtaining both multi-level samples as well as traditi...

  2. A COMPARISON OF SIX BENTHIC MACROINVERTEBRATE SAMPLING METHODS IN FOUR LARGE RIVERS

    EPA Science Inventory

    In 1999, a study was conducted to compare six macroinvertebrate sampling methods in four large (boatable) rivers that drain into the Ohio River. Two methods each were adapted from existing methods used by the USEPA, USGS and Ohio EPA. Drift nets were unable to collect a suffici...

  3. Analysis of methods commonly used in biomedicine for treatment versus control comparison of very small samples.

    PubMed

    Ristić-Djurović, Jasna L; Ćirković, Saša; Mladenović, Pavle; Romčević, Nebojša; Trbovich, Alexander M

    2018-04-01

    A rough estimate indicated that use of samples of size not larger than ten is not uncommon in biomedical research and that many of such studies are limited to strong effects due to sample sizes smaller than six. For data collected from biomedical experiments it is also often unknown if mathematical requirements incorporated in the sample comparison methods are satisfied. Computer simulated experiments were used to examine performance of methods for qualitative sample comparison and its dependence on the effectiveness of exposure, effect intensity, distribution of studied parameter values in the population, and sample size. The Type I and Type II errors, their average, as well as the maximal errors were considered. The sample size 9 and the t-test method with p = 5% ensured error smaller than 5% even for weak effects. For sample sizes 6-8 the same method enabled detection of weak effects with errors smaller than 20%. If the sample sizes were 3-5, weak effects could not be detected with an acceptable error; however, the smallest maximal error in the most general case that includes weak effects is granted by the standard error of the mean method. The increase of sample size from 5 to 9 led to seven times more accurate detection of weak effects. Strong effects were detected regardless of the sample size and method used. The minimal recommended sample size for biomedical experiments is 9. Use of smaller sizes and the method of their comparison should be justified by the objective of the experiment. Copyright © 2018 Elsevier B.V. All rights reserved.

  4. Estimation variance bounds of importance sampling simulations in digital communication systems

    NASA Technical Reports Server (NTRS)

    Lu, D.; Yao, K.

    1991-01-01

    In practical applications of importance sampling (IS) simulation, two basic problems are encountered, that of determining the estimation variance and that of evaluating the proper IS parameters needed in the simulations. The authors derive new upper and lower bounds on the estimation variance which are applicable to IS techniques. The upper bound is simple to evaluate and may be minimized by the proper selection of the IS parameter. Thus, lower and upper bounds on the improvement ratio of various IS techniques relative to the direct Monte Carlo simulation are also available. These bounds are shown to be useful and computationally simple to obtain. Based on the proposed technique, one can readily find practical suboptimum IS parameters. Numerical results indicate that these bounding techniques are useful for IS simulations of linear and nonlinear communication systems with intersymbol interference in which bit error rate and IS estimation variances cannot be obtained readily using prior techniques.

  5. A two-step electrodialysis method for DNA purification from polluted metallic environmental samples.

    PubMed

    Rodríguez-Mejía, José Luis; Martínez-Anaya, Claudia; Folch-Mallol, Jorge Luis; Dantán-González, Edgar

    2008-08-01

    Extracting DNA from samples of polluted environments using standard methods often results in low yields of poor-quality material unsuited to subsequent manipulation and analysis by molecular biological techniques. Here, we report a novel two-step electrodialysis-based method for the extraction of DNA from environmental samples. This technique permits the rapid and efficient isolation of high-quality DNA based on its acidic nature, and without the requirement for phenol-chloroform-isoamyl alcohol cleanup and ethanol precipitation steps. Subsequent PCR, endonuclease restriction, and cloning reactions were successfully performed utilizing DNA obtained by electrodialysis, whereas some or all of these techniques failed using DNA extracted with two alternative methods. We also show that his technique is applicable to purify DNA from a range of polluted and nonpolluted samples.

  6. Report: EPA Can Better Reduce Risks From Illegal Pesticides by Effectively Identifying Imports for Inspection and Sampling

    EPA Pesticide Factsheets

    Report #17-P-0412, September 28, 2017. Low rates of inspections and sampling can create a risk that the EPA may not be identifying and deterring the import of pesticides harmful to people or the environment.

  7. Rapid fusion method for the determination of Pu, Np, and Am in large soil samples

    DOE PAGES

    Maxwell, Sherrod L.; Culligan, Brian; Hutchison, Jay B.; ...

    2015-02-14

    A new rapid sodium hydroxide fusion method for the preparation of 10-20 g soil samples has been developed by the Savannah River National Laboratory (SRNL). The method enables lower detection limits for plutonium, neptunium, and americium in environmental soil samples. The method also significantly reduces sample processing time and acid fume generation compared to traditional soil digestion techniques using hydrofluoric acid. Ten gram soil aliquots can be ashed and fused using the new method in 1-2 hours, completely dissolving samples, including refractory particles. Pu, Np and Am are separated using stacked 2mL cartridges of TEVA and DGA Resin and measuredmore » using alpha spectrometry. The method can be adapted for measurement by inductively-coupled plasma mass spectrometry (ICP-MS). Two 10 g soil aliquots of fused soil may be combined prior to chromatographic separations to further improve detection limits. Total sample preparation time, including chromatographic separations and alpha spectrometry source preparation, is less than 8 hours.« less

  8. A Novel Method for Sampling Alpha-Helical Protein Backbones

    DOE R&D Accomplishments Database

    Fain, Boris; Levitt, Michael

    2001-01-01

    We present a novel technique of sampling the configurations of helical proteins. Assuming knowledge of native secondary structure, we employ assembly rules gathered from a database of existing structures to enumerate the geometrically possible 3-D arrangements of the constituent helices. We produce a library of possible folds for 25 helical protein cores. In each case the method finds significant numbers of conformations close to the native structure. In addition we assign coordinates to all atoms for 4 of the 25 proteins. In the context of database driven exhaustive enumeration our method performs extremely well, yielding significant percentages of structures (0.02%--82%) within 6A of the native structure. The method's speed and efficiency make it a valuable contribution towards the goal of predicting protein structure.

  9. Improved Butanol-Methanol (BUME) Method by Replacing Acetic Acid for Lipid Extraction of Biological Samples.

    PubMed

    Cruz, Mutya; Wang, Miao; Frisch-Daiello, Jessica; Han, Xianlin

    2016-07-01

    Extraction of lipids from biological samples is a critical step in lipidomics, especially for shotgun lipidomics where lipid extracts are directly infused into a mass spectrometer. The butanol-methanol (BUME) extraction method was originally developed to extract lipids from plasma samples with 1 % acetic acid. Considering some lipids are sensitive to acidic environments, we modified this protocol by replacing acetic acid with lithium chloride solution and extended the modified extraction to tissue samples. Although no significant reduction of plasmalogen levels in the acidic BUME extracts of rat heart samples was found, the modified method was established to extract various tissue samples, including rat liver, heart, and plasma. Essentially identical profiles of the majority of lipid classes were obtained from the extracts of the modified BUME and traditional Bligh-Dyer methods. However, it was found that neither the original, nor the modified BUME method was suitable for 4-hydroxyalkenal species measurement in biological samples.

  10. Improved Butanol-Methanol (BUME) Method by Replacing Acetic Acid for Lipid Extraction of Biological Samples

    PubMed Central

    Cruz, Mutya; Wang, Miao; Frisch-Daiello, Jessica; Han, Xianlin

    2016-01-01

    Extraction of lipids from biological samples is a critical step in lipidomics, especially for shotgun lipidomics where lipid extracts are directly infused into a mass spectrometer. The butanol-methanol (BUME) extraction method was originally developed to extract lipids from plasma samples with 1% acetic acid. Considering some lipids are sensitive to acidic environments, we modified this protocol by replacing acetic acid with lithium chloride solution and extended the modified extraction to tissue samples. Although no significant reduction of plasmalogen levels in the acidic BUME extracts of rat heart samples was found, the modified method was established to extract various tissue samples, including rat liver, heart, and plasma. Essentially identical profiles of the majority of lipid classes were obtained from the extracts of the modified BUME and traditional Bligh-Dyer methods. However, it was found that neither the original, nor the modified BUME method was suitable for 4-hydroxyalkenal species measurement in biological samples. PMID:27245345

  11. Decontamination methods for samples preserved in cetylpyridinium chloride and cultured on thin-layer agar.

    PubMed

    Ardizzoni, E; Mulders, W; Sanchez-Padilla, E; Varaine, F; de Jong, B C; Rigouts, L

    2014-08-01

    Long transportation times of samples to culture laboratories can lead to higher contamination rates and significant loss of viability, resulting in lower culture positivity rates. Thin-layer agar (TLA) is a sensitive culture method for the isolation of Mycobacterium tuberculosis that has been optimised with N-acetyl-L-cysteine-sodium hydroxide (NALC-NaOH) decontaminated samples. The combination of the TLA culture method and other decontamination procedures has not been extensively validated. Among 390 smear-positive samples, we compared the culture positivity of samples decontaminated using the Petroff method vs. NALC-NaOH neutralised with phosphate buffer (PBS), applied to samples preserved with cetylpyridinium chloride (CPC) or CPC-free, and then of CPC-preserved samples decontaminated with NALC-NaOH neutralised using Difco neutralising buffer. The sediments were inoculated on TLA, and then on MGIT 960 or Löwenstein-Jensen (LJ) as gold standards. Decontamination with NALC-NaOH yielded higher culture positivity in TLA than in the Petroff method, which was further enhanced by neutralising CPC with the Difco buffer. Surprisingly, culture positivity on LJ also increased after using Difco buffer, suggesting that CPC may not be completely neutralised in egg-based medium. After transportation in CPC, decontamination using NALC-NaOH followed by neutralisation using Difco buffer resulted in the best recovery rates for samples inoculated on TLA and on LJ.

  12. A Predictive Model for Toxicity Effects Assessment of Biotransformed Hepatic Drugs Using Iterative Sampling Method.

    PubMed

    Tharwat, Alaa; Moemen, Yasmine S; Hassanien, Aboul Ella

    2016-12-09

    Measuring toxicity is one of the main steps in drug development. Hence, there is a high demand for computational models to predict the toxicity effects of the potential drugs. In this study, we used a dataset, which consists of four toxicity effects:mutagenic, tumorigenic, irritant and reproductive effects. The proposed model consists of three phases. In the first phase, rough set-based methods are used to select the most discriminative features for reducing the classification time and improving the classification performance. Due to the imbalanced class distribution, in the second phase, different sampling methods such as Random Under-Sampling, Random Over-Sampling and Synthetic Minority Oversampling Technique are used to solve the problem of imbalanced datasets. ITerative Sampling (ITS) method is proposed to avoid the limitations of those methods. ITS method has two steps. The first step (sampling step) iteratively modifies the prior distribution of the minority and majority classes. In the second step, a data cleaning method is used to remove the overlapping that is produced from the first step. In the third phase, Bagging classifier is used to classify an unknown drug into toxic or non-toxic. The experimental results proved that the proposed model performed well in classifying the unknown samples according to all toxic effects in the imbalanced datasets.

  13. A non-uniformly under-sampled blade tip-timing signal reconstruction method for blade vibration monitoring.

    PubMed

    Hu, Zheng; Lin, Jun; Chen, Zhong-Sheng; Yang, Yong-Min; Li, Xue-Jun

    2015-01-22

    High-speed blades are often prone to fatigue due to severe blade vibrations. In particular, synchronous vibrations can cause irreversible damages to the blade. Blade tip-timing methods (BTT) have become a promising way to monitor blade vibrations. However, synchronous vibrations are unsuitably monitored by uniform BTT sampling. Therefore, non-equally mounted probes have been used, which will result in the non-uniformity of the sampling signal. Since under-sampling is an intrinsic drawback of BTT methods, how to analyze non-uniformly under-sampled BTT signals is a big challenge. In this paper, a novel reconstruction method for non-uniformly under-sampled BTT data is presented. The method is based on the periodically non-uniform sampling theorem. Firstly, a mathematical model of a non-uniform BTT sampling process is built. It can be treated as the sum of certain uniform sample streams. For each stream, an interpolating function is required to prevent aliasing in the reconstructed signal. Secondly, simultaneous equations of all interpolating functions in each sub-band are built and corresponding solutions are ultimately derived to remove unwanted replicas of the original signal caused by the sampling, which may overlay the original signal. In the end, numerical simulations and experiments are carried out to validate the feasibility of the proposed method. The results demonstrate the accuracy of the reconstructed signal depends on the sampling frequency, the blade vibration frequency, the blade vibration bandwidth, the probe static offset and the number of samples. In practice, both types of blade vibration signals can be particularly reconstructed by non-uniform BTT data acquired from only two probes.

  14. A Non-Uniformly Under-Sampled Blade Tip-Timing Signal Reconstruction Method for Blade Vibration Monitoring

    PubMed Central

    Hu, Zheng; Lin, Jun; Chen, Zhong-Sheng; Yang, Yong-Min; Li, Xue-Jun

    2015-01-01

    High-speed blades are often prone to fatigue due to severe blade vibrations. In particular, synchronous vibrations can cause irreversible damages to the blade. Blade tip-timing methods (BTT) have become a promising way to monitor blade vibrations. However, synchronous vibrations are unsuitably monitored by uniform BTT sampling. Therefore, non-equally mounted probes have been used, which will result in the non-uniformity of the sampling signal. Since under-sampling is an intrinsic drawback of BTT methods, how to analyze non-uniformly under-sampled BTT signals is a big challenge. In this paper, a novel reconstruction method for non-uniformly under-sampled BTT data is presented. The method is based on the periodically non-uniform sampling theorem. Firstly, a mathematical model of a non-uniform BTT sampling process is built. It can be treated as the sum of certain uniform sample streams. For each stream, an interpolating function is required to prevent aliasing in the reconstructed signal. Secondly, simultaneous equations of all interpolating functions in each sub-band are built and corresponding solutions are ultimately derived to remove unwanted replicas of the original signal caused by the sampling, which may overlay the original signal. In the end, numerical simulations and experiments are carried out to validate the feasibility of the proposed method. The results demonstrate the accuracy of the reconstructed signal depends on the sampling frequency, the blade vibration frequency, the blade vibration bandwidth, the probe static offset and the number of samples. In practice, both types of blade vibration signals can be particularly reconstructed by non-uniform BTT data acquired from only two probes. PMID:25621612

  15. GROUND WATER SAMPLING FOR VERTICAL PROFILING OF CONTAMINANTS

    EPA Science Inventory

    Accurate delineation of plume boundaries and vertical contaminant distribution are necessary in order to adequately characterize waste sites and determine remedial strategies to be employed. However, it is important to consider the sampling objectives, sampling methods, and sampl...

  16. A Two-Stage Method to Determine Optimal Product Sampling considering Dynamic Potential Market

    PubMed Central

    Hu, Zhineng; Lu, Wei; Han, Bing

    2015-01-01

    This paper develops an optimization model for the diffusion effects of free samples under dynamic changes in potential market based on the characteristics of independent product and presents a two-stage method to figure out the sampling level. The impact analysis of the key factors on the sampling level shows that the increase of the external coefficient or internal coefficient has a negative influence on the sampling level. And the changing rate of the potential market has no significant influence on the sampling level whereas the repeat purchase has a positive one. Using logistic analysis and regression analysis, the global sensitivity analysis gives a whole analysis of the interaction of all parameters, which provides a two-stage method to estimate the impact of the relevant parameters in the case of inaccuracy of the parameters and to be able to construct a 95% confidence interval for the predicted sampling level. Finally, the paper provides the operational steps to improve the accuracy of the parameter estimation and an innovational way to estimate the sampling level. PMID:25821847

  17. Field methods for sampling and storing nectar from flowers with low nectar volumes.

    PubMed

    Morrant, D S; Schumann, R; Petit, S

    2009-02-01

    Although several methods of sampling and storing floral nectar are available, little information exists on sampling and storing nectar from flowers with low nectar volumes. Methods for sampling and storing nectar from the flowers of species with low floral nectar volumes (<1 microL) were investigated using the flowers of Eucalyptus species. Sampling with microcapillary tubes, blotting up with filter paper, washing and rinsing were compared to determine masses of sugars recovered and differences in sugar ratios. Storage methods included room temperature, refrigeration and freezing treatments; the addition of antimicrobial agents benzyl alcohol or methanol to some of these treatments was also evaluated. Nectar samples were analysed using high-performance liquid chromatography and the masses of sucrose, glucose and fructose in each sample were determined. Masses of sugars varied significantly among sampling treatments, but the highest yielding methods, rinsing and washing, were not significantly different. A washing time of 1 min was as effective as one of 20 min. Storage trials showed that the sugar concentration measurements of nectar solutions changed rapidly, with the best results achieved for refrigeration with no additive (sucrose and fructose were stable for at least 2 weeks). Sugar ratios, however, remained relatively stable in most treatments and did not change significantly across 4 weeks for the methanol plus refrigerator and freezing treatments, and 2 weeks for the refrigeration treatment with no additive. Washing is recommended for nectar collection from flowers with low nectar volumes in the field (with the understanding that one wash underestimates the amounts of sugars present in a flower), as is immediate analysis of sugar mass. In view of the great variation in results depending on nectar collection and storage methods, caution should be exercised in their choice, and their accuracy should be evaluated. The use of pulsed amperometric detection, more

  18. Chromium speciation in environmental samples using a solid phase spectrophotometric method

    NASA Astrophysics Data System (ADS)

    Amin, Alaa S.; Kassem, Mohammed A.

    2012-10-01

    A solid phase extraction technique is proposed for preconcentration and speciation of chromium in natural waters using spectrophotometric analysis. The procedure is based on sorption of chromium(III) as 4-(2-benzothiazolylazo)2,2'-biphenyldiol complex on dextran-type anion-exchange gel (Sephadex DEAE A-25). After reduction of Cr(VI) by 0.5 ml of 96% concentrated H2SO4 and ethanol, the system was applied to the total chromium. The concentration of Cr(VI) was calculated as the difference between the total Cr and the Cr(III) content. The influences of some analytical parameters such as: pH of the aqueous solution, amounts of 4-(2-benzothiazolylazo)2,2'-biphenyldiol (BTABD), and sample volumes were investigated. The absorbance of the gel, at 628 and 750 nm, packed in a 1.0 mm cell, is measured directly. The molar absorptivities were found to be 2.11 × 107 and 3.90 × 107 L mol-1 cm-1 for 500 and 1000 ml, respectively. Calibration is linear over the range 0.05-1.45 μg L-1 with RSD of <1.85% (n = 8.0). Using 35 mg exchanger, the detection and quantification limits were 13 and 44 ng L-1 for 500 ml sample, whereas for 1000 ml sample were 8.0 and 27 ng L-1, respectively. Increasing the sample volume can enhance the sensitivity. No considerable interferences have been observed from other investigated anions and cations on the chromium speciation. The proposed method was applied to the speciation of chromium in natural waters and total chromium preconcentration in microwave digested tobacco, coffee, tea, and soil samples. The results were simultaneously compared with those obtained using an ET AAS method, whereby the validity of the method has been tested.

  19. Chromium speciation in environmental samples using a solid phase spectrophotometric method.

    PubMed

    Amin, Alaa S; Kassem, Mohammed A

    2012-10-01

    A solid phase extraction technique is proposed for preconcentration and speciation of chromium in natural waters using spectrophotometric analysis. The procedure is based on sorption of chromium(III) as 4-(2-benzothiazolylazo)2,2'-biphenyldiol complex on dextran-type anion-exchange gel (Sephadex DEAE A-25). After reduction of Cr(VI) by 0.5 ml of 96% concentrated H(2)SO(4) and ethanol, the system was applied to the total chromium. The concentration of Cr(VI) was calculated as the difference between the total Cr and the Cr(III) content. The influences of some analytical parameters such as: pH of the aqueous solution, amounts of 4-(2-benzothiazolylazo)2,2'-biphenyldiol (BTABD), and sample volumes were investigated. The absorbance of the gel, at 628 and 750 nm, packed in a 1.0 mm cell, is measured directly. The molar absorptivities were found to be 2.11×10(7) and 3.90×10(7) L mol(-1)cm(-1) for 500 and 1000 ml, respectively. Calibration is linear over the range 0.05-1.45 μg L(-1) with RSD of <1.85% (n=8.0). Using 35 mg exchanger, the detection and quantification limits were 13 and 44 ng L(-1) for 500 ml sample, whereas for 1000 ml sample were 8.0 and 27 ng L(-1), respectively. Increasing the sample volume can enhance the sensitivity. No considerable interferences have been observed from other investigated anions and cations on the chromium speciation. The proposed method was applied to the speciation of chromium in natural waters and total chromium preconcentration in microwave digested tobacco, coffee, tea, and soil samples. The results were simultaneously compared with those obtained using an ET AAS method, whereby the validity of the method has been tested. Copyright © 2012 Elsevier B.V. All rights reserved.

  20. Testing sample stability using four storage methods and the macroalgae Ulva and Gracilaria

    EPA Science Inventory

    Concern over the relative importance of different sample preparation and storage techniques frequently used in stable isotope analysis of particulate nitrogen (δ15N) and carbon (δ13C) prompted an experiment to determine how important such factors were to measured values in marine...

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