Simulation program for power and sample size determination in logistic analysis of single nucleotide polymorphisms when the response variable is subject to misclassification

The main objective of this study was to develop a simulation program to determine the sample size for a clinical study to confirm a genetic-disease association observed in a retrospective exploratory study. The effect of misclassification of a binary response variable on the power is also investigated. A general expression for the magnitude of the decrease in statistical power due to misclassification is obtained based on the Pitman asymptotic relative efficiency. The simulation program presents an estimate of the exact power when misclassification exists. Running the program several times under different settings of parameters, it revealed that the effect of even low misclassification rates is serious. Response misclassification should be taken into consideration when determining the sample size. The program can be used on the Internet.     

Numerical prediction of added mass and damping for a cylinder oscillating in confined incompressible gas–liquid two-phase mixture

This paper is concerned with the numerical analysis of the added mass and damping of a circular cylinder, which oscillates in an air–water bubbly mixture enclosed by a concentric shell. The mixture is assumed to be incompressible. This is because the oscillation frequency of the cylinder is low in this study, and accordingly the pressure change around the cylinder is not so large. An incompressible two-fluid model is solved by the finite element method, proposed by the author in a prior paper, to calculate the bubbly flow around the oscillating cylinder. The analysis reveals the effects of the diameter ratio of the cylinder to the shell, the air volumetric fraction and the bubble diameter. It also clarifies that the increase of damping ratio in the bubbly mixture is attributable to the phase lag of the drag force acting on the cylinder behind the cylinder displacement.     

Characterisation of diffuse pollutions from forested watersheds in Japan during storm events - its association with rainfall and watershed features

Forest areas have been identified as important sources of nonpoint pollution in Japan. The managers must estimate stormwater quality and quantities from forested watersheds to develop effective management strategies. Therefore, stormwater runoff loads and concentrations of 10 constituents (total suspended solids, dissolved organic carbon, PO(4)-P, dissolved total phosphorus, total phosphorus, NH(4)-N, NO(2)-N, NO(3)-N, dissolved total nitrogen, and total nitrogen) for 72 events across five regions (Aichi, Kochi, Mie, Nagano, and Tokyo) were characterised. Most loads were significantly and positively correlated with stormwater variables (total event rainfall, event duration, and rainfall intensity), but most discharge-weighted event concentrations (DWECs) showed negative correlations with rainfall intensity. Mean water quality concentration during baseflow was correlated significantly with storm concentrations (r=0.41-0.77). Although all pollutant load equations showed high coefficients of determination (R(2)=0.55-0.80), no models predicted well pollutant concentrations, except those for the three N constituents (R(2)=0.59-0.67). Linear regressions to estimate stormwater concentrations and loads were greatly improved by regional grouping. The lower prediction capability of the concentration models for Mie, compared with the other four regions, indicated that other watershed or storm characteristics should be included in the prediction models. Significant differences among regions were found more frequently in concentrations than in loads for all constituents. Since baseflow conditions implied available pollutant sources for stormwater, the similar spatial characteristics of pollutant concentrations between baseflow and stormflow conditions were an important control for stormwater quality.     

Baseflow concentrations of nitrogen and phosphorus in forested headwaters in Japan

A comprehensive investigation on all dissolved nitrogen and phosphorus components at both local and regional scales in the headwaters from forested watersheds is valuable to improve our understanding of the factors controlling water quality. Here, we investigated the baseflow concentrations of dissolved nitrogen and phosphorus components, N:P ratio, and their associations with region and vegetation type in forested headwaters in fives regions of Japan. We found that inorganic nitrogen and phosphorus were the dominant components in the 26 temperate forested streams, rather than organic forms. There were significant positive correlations between the concentrations of N and P components. Furthermore, the regional patterns of the concentrations of nitrate, dissolved inorganic P (DIP), and dissolved total N (DTN) and P (DTP) were similar. Our results suggest that the regional patterns of the concentrations of N and P components should be related to the regional atmospheric deposition of both N and P nutrients. We also found that the nitrate and DTN concentrations were higher in man-made evergreen conifer (EC) than those in the natural deciduous broadleaf (DB). In contrast, the DIP and DTP concentrations in EC were lower than those in DB. The uniformly higher N:P ratio in EC- than in DB-forested streams for each region suggest that EC-forested streams could be more affected by P-limited than DB-forested streams when N inputs from atmospheric sources increased.     

Physical Properties of Two Isomers of Conjugated Linoleic Acid

Thermal properties, powder X-ray diffraction patterns and FT-IR absorption spectra of crystals of two isomers of conjugated linoleic acid (CLA), 9-cis, 11-trans-CLA (c9t11), 10-trans, 12-cis-CLA (t10c12) were examined. To search for polymorphic modifications, we carefully performed crystallization from melt and solution phases, and isolated one type of crystalline form in c9t11 and t10c12. The melting temperature (T _m) was 14.9 °C, enthalpy of fusion (ΔH) was 38.7 kJ/mol, and entropy of fusion (ΔS) was 134 J/mol K for c9t11, and T _m = 19.8 °C, ΔH = 35.6 kJ/mol and ΔS = 122 J/mol K for t10c12. The X-ray diffraction and FT-IR measurements indicated O_⊥ subcell packing in the crystals of c9t11 and t10c12, and long spacing values of 4.22 nm for c9t11 and 3.88 nm for t10c12. The unique molecular structures of the two isomers of CLA are discussed in comparison to the polymorphism of oleic acid, petroselinic acid, elaidic acid and linoleic acid, all of which are unsaturated fatty acids having the same carbon number of 18 as that of the two CLA isomers.     

Numerical simulation for the collision between a vortex ring and solid particles

This study is concerned with the numerical simulation for the collision between a vortex ring and an ensemble of small glass particles. The vortex ring, convecting with its self-induced velocity in a quiescent air, collides with the particles. The Reynolds number for the vortex ring is 2600, and the particle diameters are 50 and 200 μm. The Stokes number St for the 50 μm particle is 0.74, while the St for the 200 μm particle is 11.4. Immediately after the collision with the vortex ring, the 50 μm particles surround the vortex ring, forming a dome. It is parallel with the preferential distribution for the particle with St ? 1 around large-scale eddies, which has been measured experimentally and simulated numerically in various free turbulent flows. The 200 μm particles disperse more due to the collision with the vortex ring. This is attributable to the centrifugal effect of large-scale eddy, which has been reported by the numerical simulation for the motion of the particle with St = 10 in a wake flow. The collision between the vortex ring and the particles induces an organized three-dimensional vortical structure. It also reduces the strength and convective velocity of the vortex ring.     

Determination method for ractopamine in swine and cattle tissues using LC/MS

Simple and reliable methods using LC/MS have been developed for the determination of the beta-agonist ractopamine in swine and cattle tissues. Ractopamine was extracted with ethyl acetate from muscle and liver, and the ethyl acetate layer was evaporated to dryness. The residue was purified by partition with acetonitrile/n-hexane. In the case of fat, ractopamine was extracted and purified by partition with acetonitrile/n-hexane. The resulting acetonitrile solutions were evaporated to dryness. The residue was dissolved in methanol, and subjected to LC/MS. The LC separation was performed on a Wakosil-II 3C18HG column (150 x 3 mm i.d.) in isocratic mode with 0.05% trifluoroacetic acid-acetonitrile (80:20) as a mobile phase at a flow rate of 0.4 mL/min. The MS detection was performed in the selected ion recording (SIR) mode, with detection of the M + H+ ion of ractopamine (m/z 302) produced by electrospray ionization (ESI). The mean recoveries of the drug from swine muscle (0.01 microg fortified), fat (0.01 microg fortified) and liver (0.04 microg/g fortified) were 99.7%, 99.5% and 100.8%, and those from cattle samples were 108.3%, 97.0% and 109.4%, respectively. The relative standard deviations (RSDs) ranged from 0.1% to 9.5%. The limit of quantification (LOQ) of the drug was 1 ng/g.     

Physicochemical characterization of densely packed poly(ethylene glycol) layer for minimizing nonspecific protein adsorption

Modification of the surface with densely packed poly(ethylene glycol) (PEG) brush layer was studied to improve the protein repellent ability of the surface. A PEG-brushed layer was constructed on a gold substrate using a PEG possessing a mercapto group at the chain end. The density of the PEG brushed layer substantially increased with repetitive adsorption/rinse cycles of the PEG on the gold substrate, allowing dramatic reduction of nonspecific protein adsorption. Notably, formation of a short, filler layer of PEG (2 kDa) in the preconstructed longer PEG brushed layer (5 kDa) achieved high density brush and almost complete prevention of nonspecific protein adsorption. On the other hand, surface modification with only long PEG chain (5 kDa) showed lower PEG brush density regardless of repetitive immobilization. Detailed characterization of the PEGylated surface was done from the physicochemical (QCM, contact angle, and SPR) as well as the biological (protein adsorption) point of view to highlight the relation between the PEG brush density and the protein repellent ability. Densely packed PEG surface which showed great protein repellent ability, presented in this study, suggests promising utility as engineered biomaterials including high-throughput screening and clinical diagnostics.     

Stable expression of a thermostable xylanase of Clostridium thermocellum in cultured tobacco cells

Two distinct domains of the xynA gene from Clostridium thermocellum encoding a xylanase catalytic domain (XynAl) and a xylanase catalytic domain with a cellulose binding domain (XynA2) under the control of the cauliflower mosaic virus 35S promoter were electroporated into cultured tobacco BY-2 cells. Transgenic BY -2 calli expressing xylan-hydrolyzing activity were obtained at high frequency for both genes. Western blot analysis using an anti-XynA antibody indicated that XynAl and XynA2 were produced in these calli.     

Effects of carbon dioxide (CO2) laser perforation as skin pretreatment to improve sugar infusion process of frozen blueberries

Sugar infusion is a widely used osmotic treatment for fruit preservation, but the process is inherently slow and the waxy skins of some fruits hinder mass transfer during the process. This work examined the utility of perforation by a carbon dioxide (CO(2)) laser as a novel skin treatment to improve the infusion process. In 2 experiments, individually quick frozen (IQF) blueberries were subjected to varying degrees of laser perforation (3 levels of perforation density × 3 levels of perforation depth), and then infused stepwise with high fructose corn syrup (HFCS) to a final °Brix of 70 using varying solution concentration increment (5, 10, 20, and 30 °Brix/d). At each concentration, increasing perforation density and depth promoted solute migration into the fruit with increased fruit weight (P < 0.05; up to 24.15%, 37.23%, 52.89%, 65.34% wt. increase at 5, 10, 20, and 30 °Brix/d compared to the controls). Laser-treated blueberries maintained the original shape without excessive shrinkage and texture hardening due to enhanced solute incorporation, while the controls and mechanically treated samples were ruptured and wrinkled at the end of the process. Increasing solution concentrations shortened the process duration but decreased final fruit weight due to greater osmotic gradients. However, negative effects of using higher solution concentrations on final fruit weight were significantly alleviated with moderate-to-high doses of laser perforation (P < 0.001). Overall, the results demonstrate that laser perforation can be a viable skin pretreatment technique, offering marked improvement on final process yield, process efficiency, and product quality. PRACTICAL APPLICATION: CO(2) laser perforation as a novel skin pretreatment for sugar infusion of individually quick frozen (IQF) blueberries is presented. The technique markedly improves the product yield and quality. Although further investigation is needed, the method may potentially be used for other waxy skin fruits such as cranberries and cherries.