Mean Value Estimation Using Two-Phase Samples with Missing Data in Both Phases

The phenomenon of nonresponse in a sample survey reduces the precision of parameter estimates and causes the bias. Several methods have been developed to compensate for these effects. An important technique is the double sampling scheme introduced by Hansen and Hurwitz (J. Am. Stat. Assoc. 41, 517–529, 1946) which relies on subsampling of nonrespondents and repeating efforts to collect data from subsampled units. Several generalizations of this procedure have been proposed, including the application of arbitrary sampling designs considered by Särndal et al. (Model Assisted Survey Sampling, 1992). Under the assumption of complete response in the second phase, the population mean estimator constructed using data from both phases is unbiased. In this paper the properties of the mean value estimator under two-phase sampling are investigated for the case of the above assumption not being met. Expressions for bias and variance are obtained for general two-phase sampling procedure involving arbitrary sampling designs in both phases. Stochastic nonresponse governed by separate response distributions in both phases is assumed. Some special cases are discussed.     

Accurate quantification of freely dissolved organochlorine pesticides in water in the presence of dissolved organic matter using triolein-embedded cellulose acetate membrane

A novel method is described using triolein-embedded cellulose acetate membrane (TECAM) for accurate determination of the freely dissolved fraction of organochlorine pesticides (OCPs) in waters rich in dissolved organic matter (DOM). The performance of the method was tested with an air-bridge system for extracting OCPs from aqueous solutions with and without humic acid. In addition, the partition coefficients between humic acid and water (K _docs) for 20 OCPs were determined by TECAM with negligible depletion extraction. Results show that TECAM predominantly extracts the freely dissolved compounds and its extraction efficiency decreases significantly with an increase in concentration of humic acid in water. The proposed methodology is suitable for facile laboratory K _doc measurement for moderate to high hydrophobic compounds (log K _ow > 4). The linear relationship between log K _ow and log K _doc obtained in this study agrees well with the results reported earlier. The kinetic uptake rate constants (k _us) and TECAM–water partition coefficients (K _TECAMs) for the 20 OCPs were obtained using the controlled laboratory continuous-flow and static exposure system, respectively. These calibration parameters were used in the field experiment to estimate the freely dissolved concentrations of OCPs in the water of Taihu Lake in China. Our results show that TECAM can be used successfully to determine the freely dissolved OCPs in aquatic environments containing DOM, and the method is particularly suited for long-term water sampling. Figure Schematic diagram of water sampling with a triolein-embedded cellulose acetate membrane (TECAM)     

Sampling of the NMR time domain along concentric rings

We present a novel approach to sampling the NMR time domain, whereby the sampling points are aligned on concentric rings, which we term concentric ring sampling (CRS). Radial sampling constitutes a special case of CRS where each ring has the same number of points and the same relative orientation. We derive theoretically that the most efficient CRS approach is to place progressively more points on rings of larger radius, with the number of points growing linearly with the radius, a method that we call linearly increasing CRS (LCRS). For cases of significant undersampling to reduce measurement time, a randomized LCRS (RLCRS) is also described. A theoretical treatment of these approaches is provided, including an assessment of artifacts and sensitivity. The analytical treatment of sensitivity also addresses the sensitivity of radially sampled data processed by Fourier transform. Optimized CRS approaches are found to produce artifact-free spectra of the same resolution as Cartesian sampling, for the same measurement time. Additionally, optimized approaches consistently yield fewer and smaller artifacts than radial sampling, and have a sensitivity equal to Cartesian and better than radial sampling. We demonstrate the method using numerical simulations, as well as a 3D HNCO experiment on protein G B1 domain.     

A Whittaker-Shannon-Kotel'nikov sampling theorem related to the Dunkl transform

A Whittaker-Shannon-Kotel'nikov sampling theorem related to the Dunkl transform on the real line is proved. To this end we state, in terms of Bessel functions, an orthonormal system which is complete in . This orthonormal system is a generalization of the classical exponential system defining Fourier series.

     

Distributions of Random Partitions and Their Applications

Assume that a random sample of size m is selected from a population containing a countable number of classes (subpopulations) of elements (individuals). A partition of the set of sample elements into (unordered) subsets, with each subset containing the elements that belong to same class, induces a random partition of the sample size m, with part sizes {Z ₁,Z ₂,...,Z _N } being positive integer-valued random variables. Alternatively, if N _j is the number of different classes that are represented in the sample by j elements, for j=1,2,...,m, then (N ₁,N ₂,...,N _m ) represents the same random partition. The joint and the marginal distributions of (N ₁,N ₂,...,N _m ), as well as the distribution of are of particular interest in statistical inference. From the inference point of view, it is desirable that all the information about the population is contained in (N ₁,N ₂,...,N _m ). This requires that no physical, genetical or other kind of significance is attached to the actual labels of the population classes. In the present paper, combinatorial, probabilistic and compound sampling models are reviewed. Also, sampling models with population classes of random weights (proportions), and in particular the Ewens and Pitman sampling models, on which many publications are devoted, are extensively presented.      

Protein folding pathways extracted by OFLOOD: Outlier FLOODing method

The Outlier FLOODing method (OFLOOD) is proposed as an efficient conformational sampling method to extract biologically rare events such as protein folding. In OFLOOD, sparse distributions (outliers in the conformational space) were regarded as relevant states for the transitions. Then, the transitions were enhanced through conformational resampling from the outliers. This evidence indicates that the conformational resampling of the sparse distributions might increase chances for promoting the transitions from the outliers to other meta‐stable states, which resembles a conformational flooding from the outliers to the neighboring clusters. OFLOOD consists of (i) detections of outliers from conformational distributions and (ii) conformational resampling from the outliers by molecular dynamics (MD) simulations. Cycles of (i) and (ii) are simply repeated. As demonstrations, OFLOOD was applied to folding of Chignolin and HP35. In both cases, OFLOOD automatically extracted folding pathways from unfolded structures with ns‐order computational costs, although µs‐order canonical MD failed to extract them. © 2014 Wiley Periodicals, Inc.     

Orthogonal sampling in free‐energy calculations of residue mutations in a tripeptide: TI versus λ‐LEUS

In a recent article (Bieler et al., J. Chem. Theory Comput. 2014, 10, 3006), we introduced a combination of λ‐dynamics and local‐elevation umbrella‐sampling termed λ‐LEUS to calculate free‐energy changes associated with alchemical processes using molecular dynamics simulations. This method was suggested to be more efficient than thermodynamic integration (TI), because the dynamical variation of the alchemical variable λ opens up pathways to circumvent barriers in the orthogonal space (defined by the N – 1 degrees of freedom that are not subjected to the sampling enhancement), a feature λ‐LEUS shares with Hamiltonian replica‐exchange (HR) approaches. However, the mutation considered, hydroquinone to benzene in water, was no real challenge in terms of orthogonal‐space properties, which were restricted to solvent‐relaxation processes. In the present article, we revisit the comparison between TI and λ‐LEUS considering non‐trivial mutations of the central residue X of a KXK tripeptide in water (with X = G, E, K, S, F, or Y). Side‐chain interactions that may include salt bridges, hydrogen bonds or steric clashes lead to slow relaxation in the orthogonal space, mainly in the two‐dimensional subspace spanned by the central and ψ dihedral angles of the peptide. The efficiency enhancement afforded by λ‐LEUS is confirmed in this more complex test system and can be attributed explicitly to the improved sampling of the orthogonal space. The sensitivity of the results to the nontrivial choices of a mass parameter and of a thermostat coupling time for the alchemical variable is also investigated, resulting in recommended ranges of 50 to 100 u nm² and 0.2 to 0.5 ps, respectively. © 2015 Wiley Periodicals, Inc.     

New QM/MM implementation of the DFTB3 method in the gromacs package

The approximate density‐functional tight‐binding theory method DFTB3 has been implemented in the quantum mechanics/molecular mechanics (QM/MM) framework of the Gromacs molecular simulation package. We show that the efficient smooth particle–mesh Ewald implementation of Gromacs extends to the calculation of QM/MM electrostatic interactions. Further, we make use of the various free‐energy functionalities provided by Gromacs and the PLUMED plugin. We exploit the versatility and performance of the current framework in three typical applications of QM/MM methods to solve biophysical problems: (i) ultrafast proton transfer in malonaldehyde, (ii) conformation of the alanine dipeptide, and (iii) electron‐induced repair of a DNA lesion. Also discussed is the further development of the framework, regarding mostly the options for parallelization. © 2015 Wiley Periodicals, Inc.     

A device for fully automated on-site process monitoring and control of trihalomethane concentrations in drinking water

An instrument designed for fully automated on-line monitoring of trihalomethane concentrations in chlorinated drinking water is presented. The patented capillary membrane sampling device automatically samples directly from a water tap followed by injection of the sample into a gas chromatograph equipped with a nickel-63 electron capture detector. Detailed studies using individual trihalomethane species exhibited method detection limits ranging from 0.01–0.04 μg L⁻¹. Mean percent recoveries ranged from 77.1 to 86.5% with percent relative standard deviation values ranging from 1.2 to 4.6%. Out of more than 5200 samples analyzed, 95% of the concentration ranges were detectable, 86.5% were quantifiable. The failure rate was less than 2%. Using the data from the instrument, two different treatment processes were optimized so that total trihalomethane concentrations were maintained at acceptable levels while reducing treatment costs significantly. This ongoing trihalomethane monitoring program has been operating for more than ten months and has produced the longest continuous and most finely time-resolved data on trihalomethane concentrations reported in the literature.     

Vacuum-assisted headspace solid phase microextraction of polycyclic aromatic hydrocarbons in solid samples

For the first time, Vacuum Assisted Headspace Solid Phase Microextraction (Vac-HSSPME) is used for the recovery of polycyclic aromatic hydrocarbons (PAHs) from solid matrices. The procedure was investigated both theoretically and experimentally. According to the theory, reducing the total pressure increases the vapor flux of chemicals at the soil surface, and hence improves HSSPME extraction kinetics. Vac-HSSPME sampling could be further enhanced by adding water as a modifier and creating a slurry mixture. For these soil-water mixtures, reduced pressure conditions may increase the volatilization rates of compounds with a low K_H present in the aqueous phase of the slurry mixture and result in a faster HSSPME extraction process. Nevertheless, analyte desorption from soil to water may become a rate-limiting step when significant depletion of the aqueous analyte concentration takes place during Vac-HSSPME. Sand samples spiked with PAHs were used as simple solid matrices and the effect of different experimental parameters was investigated (extraction temperature, modifiers and extraction time). Vac-HSSPME sampling of dry spiked sand samples provided the first experimental evidence of the positive combined effect of reduced pressure and temperature on HSSPME. Although adding 2 mL of water as a modifier improved Vac-HSSPME, humidity decreased the amount of naphthalene extracted at equilibrium as well as impaired extraction of all analytes at elevated sampling temperatures. Within short HSSPME sampling times and under mild sampling temperatures, Vac-HSSPME yielded linear calibration curves in the range of 1–400 ng g⁻¹ and, with the exception of fluorene, regression coefficients were found higher than 0.99. The limits of detection for spiked sand samples ranged from 0.003 to 0.233 ng g⁻¹ and repeatability from 4.3 to 10 %. Finally, the amount of PAHs extracted from spiked soil samples was smaller compared to spiked sand samples, confirming that soil could bind target analytes more strongly and thus decrease the readily available fraction of target analytes.