A folding artificial substratum sampler for use in standing water

A new easily retrieved folding artificial substratum sampler is described and its performance compared with that of trays in Cow Green Reservoir at a depth of 15–18 m.     

Use of 35S to determine the influence of Hexagenia on sulfur cycling in lake sediments

A new quantitative grab for sampling benthos is described. It is constructed of stainless steel to retard corrosion, and incorporates six features designed to make it outperform other grabs: 1) a frame support; 2) counter-weighted arms; 3) overlapping buckets; 4) upright posts on the frame for addition of weights; 5) a fine mesh cover on each bucket; and 6) a moving elliptical pivot point. These features result in high reliability compared to other grabs, and a somewhat quadrangular bite profile. The model in use digs to 6 cm depth over the entire area sampled, and penetrates to a maximum of 11.5 cm.     

Transport of microorganisms to Israel during Saharan dust events

Dust storms are serious meteorological events that affect the East Mediterranean region, primarily during the spring season. The physical and chemical nature of dust storms, their origin, and the meteorological conditions leading to the generation of storms have been fully documented, but knowledge on their biological content is almost nonexistent. Four dust events that occurred in the period 2004–2005 were sampled in Haifa, Israel, an urban area on the East Mediterranean coast, for biological characterization. Samples were taken before or after (depending on the meteorological conditions) as well as during the dust events. Dust particles were collected as two size fractions using a dichotomous sampler, and their elemental content was determined using X-ray fluorescence analyses. Airborne bacteria and fungi were collected with the Six Stage Andersen Viable Impactor. Fungi were identified by optical microscopy. Compared to adjacent clear days, there was an increase in the concentration of both atmospheric particles and elements of geological and marine origin during the dust events. The concentration of airborne microorganisms during the dust events was also higher, and the fungal population content was affected. On a winter clear day the abundant airborne fungi were Paecilomyces variotii, Penicillium glabrum, and Alternaria alternata. On a spring clear day, the persisting airborne fungi were Alternaria alternata, Geotrichum candidum, Penicillium chrysogenum, and P. glabrum. However, during two dust events the fungal population was dominated by Alternaria alternata, Aspergillus fumigatus, A. niger, A. thomii, Cladosporium cladosporioides, Penicillium chrysogenum, and P. griseoroseum. This study suggests that Saharan and other desert dust events in the East Mediterranean have a significant effect on the airborne microbial populations, which might impact on health, agriculture, and ecology.     

Comparative performance of contact plates,electrostatic wipes,swabs and a novel sampling device for the detection of Staphylococcus aureus on environmental surfaces

Aims

To evaluate the performance of four sampling methods [contact plates, electrostatic wipes (wipe), swabs and a novel roller sampler] for recovery of Staphylococcus aureus from a stainless steel surface.

Methods and Results

Stainless steel test plates were inoculated with Staph. aureus, dried for 24 h and sampled using each of the four methods. Samples were either incubated directly (roller, contact plate) or processed using elution and membrane filtration (swab, wipe). Performance was assessed by calculating the apparent sampling efficiency (ASE), analytical sensitivity (Sn) and percentage of replications with positive growth. The wipe demonstrated the best performance across all inoculating concentrations (ASE_48 h = 18%; Sn_48 h = 7 CFU per 100 cm²). The swab performed well when corrected for area actually sampled (ASE_48 h = 24%; Sn_48 h = 76 CFU per 100 cm²). Of the contact‐based methods, the newly developed roller sampler outperformed the contact plate (roller: ASE_48 h = 10%; Sn_48 h = 17 CFU per 100 cm²; contact plate: ASE_48 h = 0·04%; Sn_48 h = 1412 CFU per 100 cm²); both contact samplers performed better at higher inoculating concentrations (6E3 CFU per 100 cm² for the roller and 6E6 CFU per 100 cm² for the contact plate). Overall, the electrostatic wipe produced the highest number of replications resulting in positive growth (74%_24 h, 91%_48 h).

Conclusions

This study demonstrates that selection of the sampling method must be carefully considered, given that different methods have varying performance.

Significance and Impact of the Study

This is the first study assessing static wipes for sampling and one that uses a more real‐world‐relevant 24‐h drying time. The results help with infection control, and environmental health professionals choose better sampling methodologies.     

Multiple imputation for missing values through conditional Semiparametric odds ratio models

Multiple imputation is a practically useful approach to handling incompletely observed data in statistical analysis. Parameter estimation and inference based on imputed full data have been made easy by Rubin's rule for result combination. However, creating proper imputation that accommodates flexible models for statistical analysis in practice can be very challenging. We propose an imputation framework that uses conditional semiparametric odds ratio models to impute the missing values. The proposed imputation framework is more flexible and robust than the imputation approach based on the normal model. It is a compatible framework in comparison to the approach based on fully conditionally specified models. The proposed algorithms for multiple imputation through the Markov chain Monte Carlo sampling approach can be straightforwardly carried out. Simulation studies demonstrate that the proposed approach performs better than existing, commonly used imputation approaches. The proposed approach is applied to imputing missing values in bone fracture data.     

A sampling device that quantitatively collects benthos in flowing or standing waters

A hand-operated suction sampler designed to sample benthos from fine to coarse rocky substrata in standing and flowing waters is described. The suction sampler collected a similar number of taxa but more individuals from a flowing riffle than a modified Surber sampler. A critique of the suction sampler is presented, illustrating the suitability of the sampler for quantitative studies of streams with highly variable discharge or intermittency.     

Process development of methylenedioxyphenyl-acetone chiral bioreduction

Talampanel is a non-competitive antagonist of AMPA receptor, and it is a drug studied for the treatment of epilepsy and cerebrovascular ischemia. The first step of an efficient synthesis of talampanel is the reduction of 3,4-methylenedioxyphenyl-acetone (MDA) to (S)--methyl-1,3-benzodioxole-5-ethanol (MBE) accomplished with the use of Zygosaccharomyces rouxii in the presence of XAD-7 resin. Z. rouxii was chosen for its resistance to higher substrate and product concentrations (<6 g/l) and its higher reductase activity in comparison to other yeasts. Application of the moderately polar adsorbent resulted in low and non-toxic concentration of both the substrate and product in water phase.

A low cost fermentation medium without any component of animal origin was elaborated to produce Z. rouxii biomass. The control of pH and dissolved oxygen concentration, temperature, antifoam system, the time of harvest, the rate of inoculations and the number of inoculation steps were also studied. The fermentation process in 1000 l fermentor provided cell paste, possessing satisfactory ketoreductase activity (95–99%) with excellent enantioselectivity.

A method was developed to measure enzyme activity and to determine the key parameters of bioreduction. Excellent enantioselectivity was found under all conditions studied. The yield was very sensitive to the quality of cell paste. In a rather wide range temperature and aeration did not affect the results of bioreduction.     

A Bayesian approach to ordering gene markers

A technique is presented whereby a marker map can be constructed using resource family data with an entire class of missing data. The focus is on a half-sib design where there is only information on a single parent and its progeny. A Bayesian approach is utilised with solutions obtained via a Markov chain Monte Carlo algorithm. Features of the approach include the capacity to determine parameters for the ungenotyped dam population, the ability to incorporate published information and its reliability, and the production of posterior densities and the consequent deduction of a wide range of inferences. These features are demonstrated through the analysis of simulated and experimental data.     

Bayesian methods for a three-state model for rodent carcinogenicity studies

The objective of a chronic rodent bioassay is to assess the impact of a chemical compound on the development of tumors. However, most tumor types are not observable prior to necropsy, making direct estimation of the tumor incidence rate problematic. In such cases, estimation can proceed only if the study incorporates multiple interim sacrifices or we make use of simplified parametric or nonparametric models. In addition, it is widely accepted that other factors, such as weight, can be related to both dose level and tumor onset, confounding the association of interest. However, there is not typically enough information in the current study to assess such effects. The addition of historical data can help alleviate this problem. In this article, we propose a novel Bayesian semiparametric model for the analysis of data from rodent carcinogenicity studies. We develop informative prior distributions for covariate effects through the use of historical control data and outline a Gibbs sampling scheme. We implement the model by analyzing data from a National Toxicology Program chronic rodent bioassay.     

Estimation in the cox proportional hazards model with left-truncated and interval-censored data

We show that the nonparametric maximum likelihood estimate (NPMLE) of the regression coefficient from the joint likelihood (of the regression coefficient and the baseline survival) works well for the Cox proportional hazards model with left-truncated and interval-censored data, but the NPMLE may underestimate the baseline survival. Two alternatives are also considered: first, the marginal likelihood approach by extending Satten (1996, Biometrika 83, 355-370) to truncated data, where the baseline distribution is eliminated as a nuisance parameter; and second, the monotone maximum likelihood estimate that maximizes the joint likelihood by assuming that the baseline distribution has a nondecreasing hazard function, which was originally proposed to overcome the underestimation of the survival from the NPMLE for left-truncated data without covariates (Tsai, 1988, Biometrika 75, 319-324). The bootstrap is proposed to draw inference. Simulations were conducted to assess their performance. The methods are applied to the Massachusetts Health Care Panel Study data set to compare the probabilities of losing functional independence for male and female seniors.