The statistical analysis of truncated data: application to the Sverdlovsk anthrax outbreak

An outbreak of anthrax occurred in the city of Sverdlovsk in Russia in the spring of 1979. The outbreak was due to the inhalation of spores that were accidentally released from a military microbiology facility. In response to the outbreak a public health intervention was mounted that included distribution of antibiotics and vaccine. The objective of this paper is to develop and apply statistical methodology to analyse the Sverdlovsk outbreak, and in particular to estimate the incubation period of inhalational anthrax and the number of deaths that may have been prevented by the public health intervention. The data available for analysis from this common source epidemic are the incubation periods of reported deaths. The statistical problem is that incubation periods are truncated because some individuals may have had their deaths prevented by the public health interventions and thus are not included in the data. However, it is not known how many persons received the intervention or how efficacious was the intervention. A likelihood function is formulated that accounts for the effects of truncation. The likelihood is decomposed into a binomial likelihood with unknown sample size and a conditional likelihood for the incubation periods. The methods are extended to allow for a phase-in of the intervention over time. Assuming a lognormal model for the incubation period distribution, the median and mean incubation periods were estimated to be 11.0 and 14.2 days respectively. These estimates are longer than have been previously reported in the literature. The death toll from the Sverdlovsk anthrax outbreak could have been about 14% larger had there not been a public health intervention; however, the confidence intervals are wide (95% CI 0-61%). The sensitivity of the results to model assumptions and the parametric model for the incubation period distribution are investigated. The results are useful for determining how long antibiotic therapy should be continued in suspected anthrax cases and also for estimating the ultimate number of deaths in a new outbreak in the absence of any public health interventions.     

Life cycle inventory analysis of co<Subscript>2</Subscript> emissions manufacturing commodity plastics in japan

The goal of this study was to calculate the average CO₂ emissions for manufacturing three commodity plastics, polyethylene (PE), polypropylene (PP), and polyvinyl chloride (PVC) in Japan. The CO₂ emissions were calculated from cradle to gate, excluding the calcination processes after use. As the results, the followings were observed: 1) The gross CO₂ emissions for the manufacture of plastics in Japan were 1.3, 1.4, and 1.7 kg-CO₂/kg-PE, PP, and PVC, respectively. These mainly reflected the difference of CO₂ emissions for the in-house electricity generation. 2) The CO₂ emissions for the electricity used for manufacturing PVC were higher than that used for PE and PP, because additional electricity was required for the electrolysis to produce chlorine. The gross electricity consumption for manufacturing PVC was 1.3 kWh/kg-PVC, and the other plastics consumed 0.5 kWh/kg-Products. In addition, the effects of energy saving were studied using a projected gas-diffusion electrode for the electrolysis of salt on the reduction of CO₂ emissions. It was estimated that the reduction in CO₂ emissions was 7% compared with the present PVC manufacturing processes.     

Mitochondrial nitric oxide localization in H9c2 cells revealed by confocal microscopy.

This study shows the presence of all three nitric oxide synthases (NOSs) and NOS activity in H9c2 cells cultured under non-stimulated conditions. By using the 4,5 diaminofluoresceindiacetate (DAF-2DA) fluorimetric nitric oxide (NO(*)) detection system we observed NO(*) production in H9c2 cells. As revealed by confocal microscopy, NO(*) fluorescence colocalizes in mitochondria labeled with Mito-Tracker Red CM-H(2)Xros. Upon stimulation with acetylcholine (Ach), which increased NOS activity by 75%, the colocalization coefficient C(green) value, calculated as Pearson's correlation, increased from 0.07 to 0.10, demonstrating an augmented presence of NO(*) in mitochondria. Conversely, the presence of NO(*) in mitochondria decreased following cells pretreatment with l-MonoMethylArginine (L-NMMA), a competitive inhibitor of NOS activity, as indicated by the reduction of the C(green) value to 0.02. This work confirms that the presence of NO(*) in mitochondria can be modulated in response to different fluxes of NO(*).     

Growth and amino acid contents of<Emphasis Type="Italic">Spirulina platensis</Emphasis> with different nitrogen sources

The growth and amino acid contents of the cyanobacterium,Spirulina platensis strain NIES 46, were investigated using ammonium, nitrate, nitrite, or urea as the sole nitrogen source in a batch culture. Chlorophylla concentration was highest at 2,096 μg/L in the nitrate group after 10 days of cultivation, while the dry weight ofS. platensis was highest at 4.5 g/L in the ammonium group after 30 days of cultivation. The total amino acid content was highest at 174 mg/g dry weight ofS. platensis in the urea group at the end of the cultivation period, yet the amino acid patterns forS. platensis were similar for all the experimental groups. Therefore, it seemed that the growth and amino acid composition ofS. platensis varied depending on the type of nitrogen sources, while the amino acid patterns were not changed. Also, the most efficient harvesting time forS. platensis seemed to be approximately 10 days after cultivation.     

Carbon source utilization profiles as a method to identify sources of faecal pollution in water

AIMS: Carbon source utilization profiles as a phenotypic fingerprinting methodology for determining sources of faecal pollution in water were evaluated. METHODS AND RESULTS: Three hundred and sixty-five Enterococcus isolates were collected from known faecal sources in four different geographical regions and were identified to species with the commercial Biolog system. Discriminant analysis (DA) was used to identify the substrate-containing wells that best classified the 365 isolates by source. By using 30 of the 95 wells for the analysis, the average rate of correct classification (ARCC) by source was 92.7% for a human vs non-human two-way classification when isolates from all regions were combined into one library. Corresponding ARCCs for other classification schemes were 81.9% for a four-way classification of human vs livestock vs wildlife vs domestic pets, and 85.7% for a three-way classification without human isolates. When three individual libraries were made based on classification of sources within Enterococcus species, the ARCC was 95.3% for the Ent. faecalis library, 95.8% for the Ent. gallinarum library and 94.7% for the Ent. mundtii library. Thirty Enterococcus isolates (unknown sources) were obtained from each of three stream sites where a specific source of pollution was apparent; 90.0% of the isolates from a human-suspected source were classified as human, 86.6% were classified as livestock from a livestock-suspected site, and 93.3% were classified as wildlife from a wildlife-suspected site. CONCLUSIONS: Phenotypic fingerprinting with carbon source utilization profiles provided levels of correct classification by sources from an Enterococcus library that were in the upper range of those reported in the literature. ARCCs for three Enterococcus species-specific libraries were very high and may be the best approach for further developing this concept and methodology. SIGNIFICANCE ANC IMPACT OF THE STUDY: The results, based on a modest Enterococcus library and a preliminary field validation test, demonstrated the potential for carbon source utilization profiles to be employed as a phenotypic method for determining sources of faecal pollution in water.     

Effect of different starvation conditions on the flocculation of Saccharomyces cerevisiae

AIMS: To study the effect of different starvation conditions on the flocculation of an ale brewing yeast of Saccharomyces cerevisiae NCYC 1195. METHODS AND RESULTS: Flocculation was assessed by a micro-flocculation technique (Soares and Mota 1997). Carbon-starved cells of a NewFlo phenotype strain did not lose flocculation during a 48 h period. Cells incubated only in the presence of fermentable carbon sources (glucose, galactose and maltose at 2%, w/v), showed a progressive flocculation loss. The incubation of cells in 4% (v/v) ethanol did not induce a flocculation loss. The simultaneous incubation of cells in the presence of 2% (w/v) glucose and 15 microg ml(-1) cycloheximide hindered flocculation loss. The presence of 0.1 mmol l(-1) PMSF or 10 mmol l-1 EDTA prevented partially or completely, respectively, the loss of flocculation in the presence of glucose. CONCLUSIONS: Fermentable sugars induced a flocculation loss, which seems to require de novo protein synthesis and the involvement of different proteases. SIGNIFICANCE AND IMPACT OF THE STUDY: The findings reported here contribute to the elucidation of the role of nutrients on the physiological control of yeast flocculation.     

Improved production of (<Emphasis Type="Italic">S</Emphasis>)-ketoprofen ester hydrolase by a mutant of<Emphasis Type="Italic"> Trichosporon brassicae</Emphasis> CGMCC 0574

An efficient screening method following UV mutagenesis yielded a high frequency of improved mutants of Trichosporon brassicae CGMCC 0574, a wild-type esterase-producer capable of enantioselectively hydrolyzing the ethyl ester of ketoprofen [2-(3-benzoylphenyl) propionic acid]. The mutant had an activity 1.8-fold higher than the wild type and was stable in its enzyme production for ten serial transfers. As the best single carbon source, isopropanol improved the specific activity of the enzyme 5-fold; and this did not result from the effect of cell permeabilization. An 18-h culture grown on a medium containing 0.5% glucose plus 0.5% isopropanol produced 3-fold as much esterase as a culture grown on 1% glucose.     

Synthesis of (20S)-[7,7,21,21-2H4]-3beta-(tert-butyldimethylsilanyloxy)-20-methyl-pregn-5-en-21-ol,a useful intermediate for the preparation of deuterated isotopomers of sterols

(20S)-[7,7,21,21-2H(4)]-3beta-(tert-Butyldimethylsilanyloxy)-20-methyl-pregn-5-en-21-ol, an intermediate for the preparation of deuterated isotopomers of sterols to be used as standards for biomedical studies, was prepared by reduction with dichloroaluminum deuteride of ethyl (20S)-3beta-(tert-butyldimethylsilanyloxy)-7-oxo-pregn-5-en-20-carboxylate. Using controlled experimental conditions, it has also been shown that the dichloroaluminum hydride reduction of a 7-keto steroid affords the corresponding 7beta-hydroxy derivative in a highly stereoselective manner.     

Protein family alignment annotation

For bioscientists studying protein structure and function, the Protein Family Alignment Annotation Tool (Pfaat) is a useful and simple program for annotating collections of proteins. This open-source software includes methods for viewing and aligning protein families, and for annotating sequence structure and residues with known functions. It offers new options to aid the study of proteins, and an extensible annotation tool for bioinformatics developers.     

Nitrogen use efficiency by a slow-growing species as affected by CO2 levels, root temperature, N source and availability

This study examines the importance of N source and concentration on plant response to distinct CO₂ concentrations and root temperatures. The experimental design of this work was a factorial combination of: CO₂ concentration, nitrogen concentration, nitrogen source and root temperature. Carob (Ceratonia siliqua L.) was assessed as a potential model of a slow growing Mediterranean species.

The results showed that: 1) biomass increment under high CO₂ varied between 13 and 100 percnt; in relation to plants grown under the same conditions but at ambient CO₂ concentrations, depending on the root temperature and nitrogen source; 2) nitrate-fed plants attained a larger increase in biomass production compared to ammonium-fed ones. This performance seems to be linked to the co-ordinated regulation of the activities of glutamine synthetase and sucrose phosphate synthase. The variations in the magnitude and nature of growth responses to elevated CO₂ observed resulted in substantial changes in the chemical composition of the plant material and consequently in plant nitrogen use efficiency.

Although performed with seedlings and under controlled conditions, this work emphasizes the importance of the nitrogen source used by the plants, a factor rarely taken into consideration when forecasting plant responses to global changes. Particularly, the results presented here, highlight the potential for uncoupling biomass accumulation from increment of air CO₂ concentration and show that more than nitrogen availability N source may offset positive plant growth responses under elevated CO₂ and root temperature.