The Chemical Potential of Dense Liquids by the Coupled Test Particle Method

Abstract

A new method for chemical potential estimation is proposed which is based on the coupled particle approach. The coupled particle method defines an attractive solution to the weighting function problem in umbrella sampling, bridging the gap between f and g distributions at high density. A way of eliminating the origin singularity is suggested, which is similar in spirit to the restricted umbrella sampling of Shing and Gubbins, but which is based on geometric rather than energetic criteria.

The method is illustrated on the Lennard-Jones system up to a reduced density ρ? = 1.1 along the isotherm T? = 1.2 and results are compared with the test particle insertion method and empirical equations of state. The new method is particularly useful at high liquid densities where it is superior to the other methods relying on the degree of overlap of f and g distributions. It gives reliable estimates of the chemical potential in the whole range of liquid densities.     

A comparison of two methods for measuring vessel length in woody plants

Vessel lengths are important to plant hydraulic studies, but are not often reported because of the time required to obtain measurements. This paper compares the fast dynamic method (air injection method) with the slower but traditional static method (rubber injection method). Our hypothesis was that the dynamic method should yield a larger mean vessel length than the static method. Vessel length was measured by both methods in current year stems of Acer, Populus, Vitis and Quercus representing short‐ to long‐vessel species. The hypothesis was verified. The reason for the consistently larger values of vessel length is because the dynamic method measures air flow rates in cut open vessels. The Hagen–Poiseuille law predicts that the air flow rate should depend on the product of number of cut open vessels times the fourth power of vessel diameter. An argument is advanced that the dynamic method is more appropriate because it measures the length of the vessels that contribute most to hydraulic flow. If all vessels had the same vessel length distribution regardless of diameter, then both methods should yield the same average length. This supports the hypothesis that large‐diameter vessels might be longer than short‐diameter vessels in most species.     

Non-specificity of a colorimetric method for the estimation of N-acetyl-d-glucosamine

The colorimetric method of Reissig et al. for the estimation of N-acetylamino sugars, is often used as a specific method for the quantification of the N-acetyl-d-glucosamine. Although this assay is more sensitive to the monomer, it recognizes all soluble N-acetyl-d-glucosamine oligomers. This result is very important because this method is extensively used in biology for the estimation of chitinolytic activity.     

Optimising multi-tier open nucleus breeding schemes

Summary The constant migration (CM) method and the ebv migration (EBVM) method of optimising the design of multi-tier open nucleus breeding schemes are presented and compared. The equation for the equilibrium rate of genetic gain of a three-tier open nucleus scheme is determined using the CM method. The major advantage of the EBVM method is the reduction in the number of parameters which have to be varied in order to locate the maximum equilibrium rate of genetic gain. For the CM method for the number of variable parameters is 5, 14, 27 and (2n + 1) (n - 1) for unrestricted male and female migration in schemes with 2, 3, 4 and n tiers respectively. The corresponding number of variable parameters for the EBVM method is 1, 2, 3 and n-1 respectively. A procedure is given for the EBVM method so as to accomodate variance loss due to selection and variance gain due to the mixing of groups with a different mean breeding value.     

Rapid detection of total and viable Legionella pneumophila in tap water by immunomagnetic separation,double fluorescent staining and flow cytometry

We developed a rapid detection method for Legionella pneumophila (Lp) by filtration, immunomagnetic separation, double fluorescent staining, and flow cytometry (IMS‐FCM method). The method requires 120 min and can discriminate ‘viable’ and ‘membrane‐damaged’ cells. The recovery is over 85% of spiked Lp SG 1 cells in 1 l of tap water and detection limits are around 50 and 15 cells per litre for total and viable Lp, respectively. The method was compared using water samples from house installations in a blind study with three environmental laboratories performing the ISO 11731 plating method. In 53% of the water samples from different taps and showers significantly higher concentrations of Lp were detected by flow cytometry. No correlation to the plate culture method was found. Since also ‘viable but not culturable’ (VNBC) cells are detected by our method, this result was expected. The IMS‐FCM method is limited by the specificity of the used antibodies; in the presented case they target Lp serogroups 1–12. This and the fact that no Lp‐containing amoebae are detected may explain why in 21% of all samples higher counts were observed using the plate culture method. Though the IMS‐FCM method is not yet fit to completely displace the established plating method (ISO 11731) for routine Lp monitoring, it has major advantages to plating and can quickly provide important insights into the ecology of this pathogen in water distribution systems.     

Rapid method for determination of riboflavin in urine by high-performance liquid chromatography

A simple, specific, and sensitive high-performance liquid chromatographic (HPLC) method for the determination of riboflavin directly in urine samples using a fixed-wave-length spectrofluorometer is described. Centrifuged raw urine samples (50 μl) are injected onto a reversed-phase microparticulate C₁₈ column. The eluent is 0.01 M KH₂PO₄ (pH 5.0)—methanol (65:35). This method is capable of differentiating riboflavin from riboflavin-5-phosphate, non-riboflavin fluorescing components in urine, and photo-degraded riboflavin. The method shows good reproducibility and is linear to at least 12 μg/ml. The sensitivity of this procedure, at the 95% confidence limit, determined by linear regression analysis, is estimated to be 0.05 μg/ml using peak height and 0.07 μg/ml using peak area. This HPLC method is compared to an automated fluorometric method for riboflavin. The coefficient of linear regression of this comparison is Y = 0.858 + 0.893X, where X is the HPLC method and Y is the fluorometric method.     

Comparison of Zinc Reduction with Platinum Reduction for Analysis of Deuterium‐Enriched Water Samples for the Doubly Labeled Water Technique

Objective: Isotope ratio mass spectrometry of hydrogen and oxygen is frequently used to determine total energy expenditure (TEE) using doubly labeled water. Conventionally, hydrogen isotope ratio is determined in hydrogen gas generated from water samples using zinc reduction. We compare this with a new automated platinum method to determine the ratios of hydrogen isotopes in deuterium‐enriched water samples. Research Methods and Procedures: The platinum method of sample preparation was compared with the zinc method in three ways: analytical variation in deuterium enrichment (within sample; n = 51), analytical variation in TEE estimates (within sample set; n = 10), and level of agreement of TEE estimates between both methods (n = 14). Results: For the zinc method, the standard deviation for multiple sets of triplicate ²H₂O sample analysis was ±4.36‰ and ±2.07‰ for platinum. The correlation between TEE estimates when sample sets were analyzed in duplicate was r = 0.89 for zinc and r = 0.83 for platinum. The intercept and slope of the regression line were significantly different from the line of identity for duplicate TEE estimates by zinc but were not different from the line of identity for platinum. After correction for the intra‐assay variation of each method, the correlation between zinc and platinum for TEE was 0.77, and the intercept, but not the slope, of the regression was significantly different from the line of identity. The mean difference between the zinc method and the platinum method was 56 kcal/day, and the 95% confidence interval was ?438 to 550 kcal/day. Discussion: These data suggest that the platinum method is at least as reliable as the zinc method as a sample preparation technique for isotope ratio mass spectrometry of deuterium‐enriched water samples. The platinum method is also less costly and less labor‐intensive than the zinc method.     

Comparison of swabbing and destructive methods for microbiological pig carcass sampling

Aims: To compare the Belgian swabbing sampling method for pig carcasses with the reference destructive method with regard to Escherichia coli and aerobic plate counts, Salmonella and Campylobacter prevalence and their relationship. Methods and Results: Recovery was significantly lower for the swabbing method and corresponded to a recovery of 36% for E. coli counts and 81% for aerobic plate counts in comparison with the destructive method. There was no significant difference between the swabbing and destructive sampling methods for the prevalence of Salmonella or Campylobacter. A higher median for E. coli counts was detected for samples where Salmonella or Campylobacter were detected. The same association was also observed between the median for aerobic plate counts and the presence of Campylobacter. Conclusions: The method of swabbing used, covering 600 cm² on each half‐pig carcass, is efficient for the sampling of pig carcasses in comparison with the reference destructive method. Significance and Impact of the Study: This study describes an efficient method for microbiological pig carcass sampling. The Belgian swabbing method should continue to be used to allow the follow up of bacterial contamination in the Belgian meat production chain.     

Methods for quantitative sampling of epiphytic microinvertebrates in lake vegetation

 Two methods were developed for the quantitative sampling of rotifers and cladocerans attached to aquatic macrophytes while separating them from plankton. We named them the “covering method” and the “picking-up method.” We consider the covering method to be better for estimating the abundance of animals on plants, but it requires hard work on a boat. In contrast, the picking-up method is simple and easy to perform, but it seems to estimate animal abundance with some errors. The densities of rotifers and cladocerans on emergent and submerged plants in two Japanese lakes were estimated by the two methods, and the results were compared. The densities of most animals (e.g., the rotiferans Brachionus, Mytilina, Lepadella, and Colurella, and the cladoceran Alona) estimated by the picking-up method did not differ from those estimated by the covering method. In contrast, the densities of the rotiferans Monostyla, Euchlanis, and Trichocerca estimated by the picking-up method tended to be lower than those estimated by the covering method. These suggest that the picking-up method is suitable for estimating many densities, except for some rotiferan genera. Received: August 29, 2001 / Accepted: February 15, 2002     

Applications of phasors to in vitro time-resolved fluorescence measurements

The phasor method of treating fluorescence lifetime data provides a facile and convenient approach to characterize lifetime heterogeneity and to detect the presence of excited state reactions such as solvent relaxation and Förster resonance energy transfer. The method uses a plot of M sin(Φ) versus M cos(Φ), where M is the modulation ratio and Φ is the phase angle taken from frequency domain fluorometry. A principal advantage of the phasor method is that it provides a model-less approach to time-resolved data amenable to visual inspection. Although the phasor approach has been recently applied to fluorescence lifetime imaging microscopy, it has not been used extensively for cuvette studies. In the current study, we explore the applications of the method to in vitro samples. The phasors of binary and ternary mixtures of fluorescent dyes demonstrate the utility of the method for investigating complex mixtures. Data from excited state reactions, such as dipolar relaxation in membrane and protein systems and also energy transfer from the tryptophan residue to the chromophore in enhanced green fluorescent protein, are also presented.     

Approximate Confidence Interval on Ratio of Two Variances in a Two-way Crossed Model

The model considered is a two-factor cross-classification variance components model with one observation per cell. Let the two factors be A and B, the problem is to obtain an approximate confidence interval for the ratio of variance component A over variance component B. In this paper, a method of solving this problem is established and simulations are performed to check the method.     

Evaluation of agar diffusion bioassay for nisin quantification

The agar diffusion bioassay is the most widely used method for the quantification of nisin, due to its high sensitivity, simplicity, and cost-effectiveness. This method is based on the measurement of the inhibition zone produced in nisin-sensitive microorganisms. The size of the zone is affected by many factors, such as nisin-sensitive strain, amount of added agar and surfactant, and pre-diffusion step. This research aims to evaluate the effects of nisin-sensitive strains and pre-diffusion on the accuracy and precision of nisin quantification. Three strains of nisin-sensitive microorganisms (Micrococcus luteus, Lactobacillus sakei, Brochothrix thermosphacta) were tested along with three different incubation processes. The best combination was the method using L. sakei as an indicator strain with pre-diffusion at 4 °C for 24 h. Compared with M. luteus and B. thermosphacta, L. sakei gave more accurate and reproducible results. Moreover, the pre-diffusion step resulted in larger inhibition zones and more precise results. Finally, the best combination was validated and compared with the method that is usually used and the result showed that the method using L. sakei with pre-diffusion gave more accurate and precise results.     

Theory and practice of the analytical centrifugation of an active substrate-enzyme complex

The active enzyme centrifugal-ion (AEC) method presented here permits the hydrodynamic study of active enzyme–substrate(s) complexes in solutions containing micro-gram amounts of the studied enzyme, even if the enzyme preparation is very impure. The AEC method can he used only when the specific enzymatie reaction can be measured directly in a spectrophotometer. The general equations relevant to the method and their solutions are presented in detail. Their use requires some numerical calculations. A practical summary of the AEC method is given, and the precision of the measured values of the sedimentation and diffusion coefficients is discussed.     

Determination of 5-aminolevulinic acid in blood plasma, tissues and cell cultures by high-performance liquid chromatography with electrochemical detection

A simple and sensitive method for determining 5-aminolevulinic acid (ALA) in biological samples is described. ALA is derivatized with o-phthaldehyde to give a compound with favorable properties for high-performance liquid chromatography with electrochemical detection. The method does not require extensive pretreatment of the samples and its detection limit is in the range of 1 pmol/20 μl injection. This method was applied to the determination of plasma ALA from normal and lead-exposed subjects, where 0.26±0.08 μM (n=30) and 2.6±0.75 μM (n=30), respectively were found. We also determined ALA in rat tissues, namely liver and brain, and the uptake of ALA by cultured fibroblasts and hepatocytes to illustrate the diversified applicability of the method.     

Levofloxacin susceptibility testing for Helicobacter pylori in China: comparison of E-test and disk diffusion method

Background: The aims of this study were to compare disk diffusion with E‐test method for levofloxacin susceptibility testing of Helicobacter pylori and standardized breakpoints for disk diffusion as a stable and reliable method for determining qualitative levofloxacin susceptibility. Materials and Methods: We determined the levofloxacin susceptibility of 45 H. pylori strains isolated from Chinese patients by the E‐test method. Disk diffusion was evaluated as an alternative method to determine susceptibility and compared with the E‐test results by linear regression analysis. Results: The minimum inhibitory concentration (MIC) values tested by E‐test method ranged from 0.047 to 32 μg/mL. Resistance to levofloxacin was detected in 16 (35.6%) isolates. The levofloxacin disk zone sizes obtained by disk diffusion method correlated well (r² = .877) with the MICs obtained by E‐test method. As a consequence of regression analysis, isolates with inhibition diameters <12 mm were considered resistant to levofloxacin. There was 100% agreement between the two methods for levofloxacin, applying the regression‐based breakpoints. Conclusions: The disk diffusion method is equivalent to the E‐test method for testing levofloxacin susceptibility of H. pylori strains; it is more practical and inexpensive, and it is suitable for the analysis of a small number of isolates compared with the E‐test method.     

NetCTLpan: pan-specific MHC class I pathway epitope predictions

Reliable predictions of immunogenic peptides are essential in rational vaccine design and can minimize the experimental effort needed to identify epitopes. In this work, we describe a pan-specific major histocompatibility complex (MHC) class I epitope predictor, NetCTLpan. The method integrates predictions of proteasomal cleavage, transporter associated with antigen processing (TAP) transport efficiency, and MHC class I binding affinity into a MHC class I pathway likelihood score and is an improved and extended version of NetCTL. The NetCTLpan method performs predictions for all MHC class I molecules with known protein sequence and allows predictions for 8-, 9-, 10-, and 11-mer peptides. In order to meet the need for a low false positive rate, the method is optimized to achieve high specificity. The method was trained and validated on large datasets of experimentally identified MHC class I ligands and cytotoxic T lymphocyte (CTL) epitopes. It has been reported that MHC molecules are differentially dependent on TAP transport and proteasomal cleavage. Here, we did not find any consistent signs of such MHC dependencies, and the NetCTLpan method is implemented with fixed weights for proteasomal cleavage and TAP transport for all MHC molecules. The predictive performance of the NetCTLpan method was shown to outperform other state-of-the-art CTL epitope prediction methods. Our results further confirm the importance of using full-type human leukocyte antigen restriction information when identifying MHC class I epitopes. Using the NetCTLpan method, the experimental effort to identify 90% of new epitopes can be reduced by 15% and 40%, respectively, when compared to the NetMHCpan and NetCTL methods. The method and benchmark datasets are available at .     

Application of a colorimetric DNA-DNA hybridization method for identification ofAeromonas genomic species,isolated from diarrheal stools

The colorimetric DNA-DNA hybridization method for the identification of 18 strains ofAeromonas spp. isolated from human stools was used. Bacterial isolates were also examined by phenotypic characteristics. On the basis of biochemical tests 13 strains were included in phenogroupA. caviœ and 5 strains inA. sobria. Identification to the species level was obtained by colorimetric hybridization method. DNA-DNA similarity values showed that isolates ofA. caviœ group belong to hybridization group (HG) 4 whereas isolates ofA. sobria belong to HG 8/10. DNA relatedness results obtained by the colorimetric method showed good agreement with values detected by the spectrophotometric method. The background in the colorimetric method is lower than in the spectrophotometric one. Results of this study indicate the usefulness of the colorimetric DNA-DNA hybridization in microplates method for the identification ofAeromonas genomic species, isolated from human diarrheal stools.     

Validation and rapid extraction of nucleic acids from alcohol-preserved ticks

A method has been developed to extract DNA from alcohol-preserved ticks (Acari: Ixodidae and Argasidae). The method combines the lysing property of the chaotropic agent guanidinium thiocyanate (GuSCN) and the nucleic acid-binding property of diatomaceous earth (fossilized cell walls of unicellular algae). Debris from the tick is removed in several sequential washing steps. To monitor the efficiency of this method, a polymerase chain reaction (PCR) was designed to amplify the 16S mt rRNA gene of five tick genera (Dermacentor Fabricius, Haemaphysalis Koch, Rhipicephalus Koch, Argas Latreille and Ixodes Latreille). Detection of amplification products from this PCR indicated that DNA had been successfully extracted and that Taq-polymerase inhibitors were absent. The extraction method, therefore, enables purification of DNA such that enzymatic analysis is possible.     

Tests of Independence and Zero Correlations Among P Random Variables

Suppose it is desired to determine whether there is an association between any pair of p random variables. A common approach is to test H₀ : R = I, where R is the usual population correlation matrix. A closely related approach is to test H₀ : R_pb = I, where R_pb is the matrix of percentage bend correlations. In so far as type I errors are a concern, at a minimum any test of H₀ should have a type I error probability close to the nominal level when all pairs of random variables are independent. Currently, the Gupta-Rathie method is relatively successful at controlling the probability of a type I error when testing H₀: R = I, but as illustrated in this paper, it can fail when sampling from nonnormal distributions. The main goal in this paper is to describe a new test of H₀: R_pb = I that continues to give reasonable control over the probability of a type I error in the situations where the Gupta-Rathie method fails. Even under normality, the new method has advantages when the sample size is small relative to p. Moreover, when there is dependence, but all correlations are equal to zero, the new method continues to give good control over the probability of a type I error while the Gupta-Rathie method does not. The paper also reports simulation results on a bootstrap confidence interval for the percentage bend correlation.