Prevalence of Opisthorchis viverrini-Like Fluke Infection in Ducks in Binh Dinh Province, Central Vietnam

Following the first report of Opisthorchis viverrini infection in a domestic duck in Phu My District of Binh Dinh Province, Central Vietnam, many other cases were observed in the province. We determined the infection rate and intensity of O. viverrini infection in ducks in 4 districts of the province. A total of 178 ducks were randomly selected from 34 farms for examination of flukes in the liver and gall bladder. An infection rate of 34.3% (range 20.7-40.4% among districts) was found; the intensity of infection was 13.8 worms per infected duck (range 1-100). These findings show the role of ducks as a host for O. viverrini, duck genotype, which is sympatric with the human O. viverrini genotype in this province. It also stresses the need for investigations on the zoonotic potential and the life cycle of this parasite.

Exploring the connections between green economy and informal economy in South Africa

Abstract The notion of an inclusive green economy in the context of sustainable development and poverty eradication requires an approach that engages with the informal economy. However, the informal economy is generally ignored or undervalued in discussions on the green economy. This paper set out to bolster this argument by identifying the ways in which the green economy and the informal economy may be connected by establishing the extent to which policies and plans relating to green economy connect with the informal economy, and recognising several informal green activities. The barriers and opportunities for connecting the two spheres were also explored as well as possible ways in which such activities may be supported at different levels of organisation. In the case of South Africa, many informal green activities that contribute to sustainable livelihoods are recognised. However, issues pertaining to procedure, process and participation hinder the transition to a truly inclusive green economy.

Nutrikinetic modeling reveals order of genistein phase II metabolites appearance in human plasma

SCOPE

Genistein from foods or supplements is metabolized by the gut microbiota and the human body, thereby releasing many different metabolites into systemic circulation. The order of their appearance in plasma and the possible influence of food format are still unknown. This study compared the nutrikinetic profiles of genistein metabolites.

METHODS AND RESULTS

In a randomized cross-over trial, 12 healthy young volunteers were administered a single dose of 30 mg genistein provided as a genistein tablet, a genistein tablet in low fat milk, and soy milk containing genistein glycosides. A high mass resolution LC-LTQ-Orbitrap FTMS platform detected and quantified in human plasma: free genistein, seven of its phase-II metabolites and 15 gut-derived metabolites. Interestingly, a novel metabolite, genistein-4'-glucuronide-7-sulfate (G-4'G-7S) was identified. Nutrikinetic analysis using population-based modeling revealed the order of appearance of five genistein phase II metabolites in plasma: (1) genistein-4',7-diglucuronide, (2) genistein-7-sulfate, (3) genistein-4'-sulfate-7-glucuronide, (4) genistein-4'-glucuronide, and (5) genistein-7-glucuronide, independent of the food matrix.

CONCLUSION

The conjugated genistein metabolites appear in a distinct order in human plasma. The specific early appearance of G-4',7-diG suggests a multistep formation process for the mono and hetero genistein conjugates, involving one or two deglucuronidation steps.

Detection of viral RNA by RT-PCR from serum for molecular diagnosis of measles

Measles continues to be a cause of morbidity and mortality in Côte d'Ivoire although the death rates are weak (2.4%). The monitoring and elimination programme of this disease require a laboratory confirmation testing by diverse methods of diagnosis needing diverse biological products. Serum is usually used for IgM detection. This study has therefore assessed the importance of the measles virus RNA detection from sera of measles suspected cases for confirmation of the case and determination of the genotype. A total of 45 sera tested were split into two groups according to the interval between the rash appearance and the day of blood collection: Group 1 (day 1 to day 3); group (2 day 4 to day 7). Four sera from Group 1 of the 45 (8.9 %) were positive by RT-PCR technique while 10 (22.2%) sera were positive for IgM anti- measles virus by ELISA test. RT-PCR and ELISA showed the same performance in group 1 with a positivity rate of 13.79 %. The B3 genotype was found. This result showed that the viral RNA can be detected in the serum but only from those sera collected the first 3 days after the rash appearance and could be used as palliative in case it is impossible to obtain other biological products.

The photographer and the greenhouse: how to analyse plant metabolomics data

INTRODUCTION

Plant metabolomics experiments yield large amounts of data, too much to be interpretable by eye. Multivariate data analyses are therefore essential to extract and visualise the information of interest.

OBJECTIVE

Because multivariate statistical methods may be remote from the expertise of many scientists working in the metabolomics field, this overview provides a step-by-step description of a multivariate data analysis, starting from the experiment and ending with the figures appearing in scientific journals.

METHODOLOGY

We developed a thought experiment that explores the relationship between the differences in nutrient levels and three plant developmental descriptors through photography of the greenhouse they grow in. Through this, multivariate data analysis, data preprocessing and model validation are illustrated. Finally some of the presented methods are illustrated by the analysis of a plant metabolomics dataset.

CONCLUSION

This paper will familiarize non-specialised researchers with the main concepts in multivariate data analysis and allow them to develop and evaluate metabolomic data analyses more critically.

RNA structure prediction from evolutionary patterns of nucleotide composition

Structural elements in RNA molecules have a distinct nucleotide composition, which changes gradually over evolutionary time. We discovered certain features of these compositional patterns that are shared between all RNA families. Based on this information, we developed a structure prediction method that evaluates candidate structures for a set of homologous RNAs on their ability to reproduce the patterns exhibited by biological structures. The method is named SPuNC for ‘Structure Prediction using Nucleotide Composition’. In a performance test on a diverse set of RNA families we demonstrate that the SPuNC algorithm succeeds in selecting the most realistic structures in an ensemble. The average accuracy of top-scoring structures is significantly higher than the average accuracy of all ensemble members (improvements of more than 20% observed). In addition, a consensus structure that includes the most reliable base pairs gleaned from a set of top-scoring structures is generally more accurate than a consensus derived from the full structural ensemble. Our method achieves better accuracy than existing methods on several RNA families, including novel riboswitches and ribozymes. The results clearly show that nucleotide composition can be used to reveal the quality of RNA structures and thus the presented technique should be added to the set of prediction tools.

Multilevel data analysis of a crossover designed human nutritional intervention study

A new method is introduced for the analysis of 'omics' data derived from crossover designed drug or nutritional intervention studies. The method aims at finding systematic variations in metabolic profiles after a drug or nutritional challenge and takes advantage of the crossover design in the data. The method, which can be considered as a multivariate extension of a paired t test, generates different multivariate submodels for the between- and the within-subject variation in the data. A major advantage of this variation splitting is that each submodel can be analyzed separately without being confounded with the other variation sources. The power of the multilevel approach is demonstrated in a human nutritional intervention study which used NMR-based metabolomics to assess the metabolic impact of grape/wine extract consumption. The variations in the urine metabolic profiles are studied between and within the human subjects using the multilevel analysis. After variation splitting, multilevel PCA is used to investigate the experimental and biological differences between the subjects, whereas a multilevel PLS-DA model is used to reveal the net treatment effect within the subjects. The observed treatment effect is validated with cross model validation and permutations. It is shown that the statistical significance of the multilevel classification model ( p << 0.0002) is a major improvement compared to a ordinary PLS-DA model ( p = 0.058) without variation splitting. Finally, rank products are used to determine which NMR signals are most important in the multilevel classification model.

Biomarkers for lysosomal storage disorders: identification and application as exemplified by chitotriosidase in Gaucher disease

A biomarker is an analyte that indicates the presence of a biological process linked to the clinical manifestations and outcome of a particular disease. An ideal biomarker provides indirect but ongoing determinations of disease activity. In the case of lysosomal storage disorders (LSDs), metabolites or proteins specifically secreted by storage cells are good candidates for biomarkers. Potential clinical applications of biomarkers are found in improved diagnosis, monitoring of disease progression and assessment of therapeutic correction. These applications are illustrated by reviewing the use of plasma chitotriosidase in the clinical management of patients with Gaucher disease, the most common LSD. The ongoing debate on the value of biomarkers in patient management is addressed. Novel analytical methods have revolutionized the identification and measurement of biomarkers at the protein and metabolite level. Recent developments in biomarker discovery by proteomics are described and the future for biomarkers of LSDs is discussed.

CONCLUSION

Besides direct applications for biomarkers in patient management, biomarker searches are likely to render new insights into pathophysiological mechanisms and metabolic adaptations, and may provide new targets for therapeutic intervention.

How to distinguish healthy from diseased? Classification strategy for mass spectrometry-based clinical proteomics

SELDI-TOF-MS is rapidly gaining popularity as a screening tool for clinical applications of proteomics. Application of adequate statistical techniques in all the stages from measurement to information is obligatory. One of the statistical methods often used in proteomics is classification: the assignment of subjects to discrete categories, for example healthy or diseased. Lately, many new classification methods have been developed, often specifically for the analysis of X-omics data. For proteomics studies a good strategy for evaluating classification results is of prime importance, because usually the number of objects will be small and it would be wasteful to set aside part of these as a 'mere' test set. The present paper offers such a strategy in the form of a protocol which can be used for choosing among different statistical classification methods and obtaining figures of merit of their performance. This paper also illustrates the usefulness of proteomics in a clinical setting, serum samples from Gaucher disease patients, when used in combination with an appropriate classification method.

Assessing the statistical validity of proteomics based biomarkers

A strategy is presented for the statistical validation of discrimination models in proteomics studies. Several existing tools are combined to form a solid statistical basis for biomarker discovery that should precede a biochemical validation of any biomarker. These tools consist of permutation tests, single and double cross-validation. The cross-validation steps can simply be combined with a new variable selection method, called rank products. The strategy is especially suited for the low-samples-to-variables-ratio (undersampling) case, as is often encountered in proteomics and metabolomics studies. As a classification method, principal component discriminant analysis is used; however, the methodology can be used with any classifier. A dataset containing serum samples from Gaucher patients and healthy controls serves as a test case. Double cross-validation shows that the sensitivity of the model is 89% and the specificity 90%. Potential putative biomarkers are identified using the novel variable selection method. Results from permutation tests support the choice of double cross-validation as the tool for determining error rates when the modelling procedure involves a tuneable parameter. This shows that even cross-validation does not guarantee unbiased results. The validation of discrimination models with a combination of permutation tests and double cross-validation helps to avoid erroneous results which may result from the undersampling.

Evolutionary rates vary among rRNA structural elements

Understanding patterns of rRNA evolution is critical for a number of fields, including structure prediction and phylogeny. The standard model of RNA evolution is that compensatory mutations in stems make up the bulk of the changes between homologous sequences, while unpaired regions are relatively homogeneous. We show that considerable heterogeneity exists in the relative rates of evolution of different secondary structure categories (stems, loops, bulges, etc.) within the rRNA, and that in eukaryotes, loops actually evolve much faster than stems. Both rates of evolution and abundance of different structural categories vary with distance from functionally important parts of the ribosome such as the tRNA path and the peptidyl transferase center. For example, fast-evolving residues are mainly found at the surface; stems are enriched at the subunit interface, and junctions near the peptidyl transferase center. However, different secondary structure categories evolve at different rates even when these effects are accounted for. The results demonstrate that relative rates and patterns of evolution are lineage specific, suggesting that phylogenetically and structurally specific models will improve evolutionary and structural predictions.

Evaluating the evaluators: interrater reliability on EMT licensing examinations

INTRODUCTION

Current methods of evaluating the technical competence of Michigan emergency medical technician (EMT) licensure candidates are subjective and potentially unreliable. Evaluators are required to attend a workshop before evaluating practical examination candidates. Despite the workshop, there is too much score variation and not enough observational consistency on the standardized examination.

OBJECTIVE

To determine the level of rater reliability for evaluators of EMT practical examinations.

METHODS

Data were collected from 104 licensed instructor-coordinators (ICs). Participants watched and scored two practical examinations simulated on videotape, one passing and one failing performance. Variation in student score and level of evaluator agreement concerning skill performance were determined. Michigan's basic EMT practical examination scoring instrument was used.

RESULTS

Nine basic EMT, 9 EMT specialist, and 86 EMT-paramedic ICs participated. Thirty-four percent had high school diplomas, 43% associate's degrees, 19% bachelor's degrees, 3% master's degrees, and 1% a doctoral degree. The ICs averaged 14 years of provider experience, and 6.35 years as an IC. The average score for scenario 1 (passing) was 86.4% (SD = 9.15, range = 53). An 80% score is required to pass. Nine ICs (9%) failed the student. Scenario 1 evaluator agreement was 79.4%. The average score for scenario 2 (failing) was 60.9% (SD = 11.57, range = 57). Seventeen ICs (18%) gave the student a passing score. Scenario 2 evaluator agreement was 67.8%. There was no significant difference in student scores based on evaluator level of education, licensure, or evaluator workshop attendance for either scenario.

CONCLUSION

Notable variation in scores given by evaluators for a single observed student, combined with low levels of evaluator agreement about skill performance, suggests that evaluators do not reliably rate student performance using the Michigan practical examination instrument.

The effect of manure and litter handling and indoor climatic conditions on ammonia emissions from a battery cage and an aviary housing system for laying hens

Ammonia emissions from both traditional and new welfare-based housing systems for laying hens must be reduced to prevent detrimental effects on the environment. In a comparative study, the effect of manure handling (variation in drying and removal frequency) in a battery cage and the effect of manure handling (as in battery cage system) and litter treatment (removal of litter) in a Tiered Wire Floor (TWF) aviary system on the emission of ammonia were investigated. Each system housed 6480 hens, treatments were varied in time, and effects were analysed by means of time-series analysis. The hens in the TWF system dropped 22.5% of their excreta in the litter and the remaining part, like all manure in the battery cage system, was dropped on the manure belts. The estimated emission from the manure on the belts in both systems was 18.8 g/h (daily mean, manure removal twice a day), whereas the emission from the litter in the TWF system amounted to 62.5 g/h. Emission from the belt manure on a typical day increased by 14, 39, 109 and 177% from the 1st until the 4th day after manure removal. The effect of increasing temperature and water vapour pressure difference on emission was +17% and -22% per degree and per kPa, respectively. Drying of manure on the belts increased the dry matter content of the manure and showed a tendency towards lower emissions. The dry matter content of the litter varied between 780 and 840 g/kg, the mean total nitrogen content was 3.3% of the dry matter, and the layer thickness varied between 2 and 9 cm. Both the ammonia content, which ranged between 20 and 190 mg/kg, and the layer thickness of the litter influenced the emission from the litter positively.

Control of cAMP-induced gene expression by divergent signal transduction pathways

A compilation of literature data and recent experiments led to the following conclusions regarding cyclic adenosine 3':5' monophosphate (cAMP) regulation of gene expression. Several classes of cAMP-induced gene expression can be discriminated by sensitivity to stimulation kinetics. The aggregation-related genes respond only to nanomolar cAMP pulses. The prestalk-related genes respond both to nanomolar pulses and persistent micromolar stimulation. The prespore specific genes respond only to persistent micromolar stimulation. The induction of the aggregation- and prestalk-related genes by nanomolar cAMP pulses may share a common transduction pathway, which does not involve cAMP, while involvement of the inositol 1,4,5-trisphosphate (IP3)/Ca2+ pathway is unlikely. Induction of the expression of prespore and prestalk-related genes by micromolar cAMP stimuli utilizes divergent signal processing mechanisms. cAMP-induced prespore gene expression does not involve cAMP and probably also not cyclic guanosine 3'.5' monophosphate (cGMP) as intracellular intermediate. Involvement of cAMP-induced phospholipase C (PLC) activation in this pathway is suggested by the observation that IP3 and 1,2-diacylglycerol (DAG) can induce prespore gene expression, albeit in a somewhat indirect manner and by the observation that Li+ and Ca2+ antagonists inhibit prespore gene expression. Cyclic AMP induction of prestalk-related gene expression is inhibited by IP3 and DAG and promoted by Li+, and is relatively insensitive to Ca2+ antagonists, which indicates that PLC activation does not mediate prestalk-related gene expression. Neither prespore nor prestalk-related gene expression utilizes the sustained cAMP-induced pHi increase as intracellular intermediate.

Relations among self-esteem, depression and anxiety of children

930 boys and girls enrolled in Grades 2 through 9 participated in a study of the relations among self-esteem, depression, and anxiety. The criterion measures correlated significantly for all children, boys and girls in both elementary and junior high groups. Depression correlated higher with total self-esteem for all children, boys and girls in elementary and junior high school groups.

Iron uptake by Chinese hamster fibroblasts from human transferrin

The manner of uptake or iron by Chinese hamster fibroblasts, type DON, from human transferrin was investigated by means of replacement studies, in which the cells that were incubated with 125I-labelled human transferrin were chased with non-radioactive transferrin for only a few minutes. The results did not support the reversible endocytosis hypothesis for the uptake of iron from transferrin. The uptake of iron measured as 59Fe during several cell divisions was found to be a function of time and cell number. It was found that the total uptake of iron in the harvests was directly proportional to the incubation, and that the uptake per 10(6) cells levelled off in the course of time.

Polynuclear iron compounds in human transferrin preparations

During commonly used saturation procedures of transferrin with iron compounds, both as ferri and ferrous, polynuclear iron compounds are easily formed, even when nitrilotriacetate (NTA) is used as a strong iron ligand. The presence of these nonspecific bound irons is demonstrated with Mossbauer spectroscopy and with electronic optical spectroscopy. But no evidence, however, has been found of two different iron binding sites. Because dialysis is not able to remove all polynuclear iron, an easy method with gel filtration has been developed that does remove the polynuclear iron. Some notes are made about the often used method, in transferrin biochemistry, of saturation determination, i.e. the quotient of the absorbances of 470 and 280 nm.

Analysis of the urine of the okapi (Okapia johnstoni)

The urine of six adult and two juvenile okapis housed in The Royal Rotterdam Zoological and Botanical Gardens were analysed qualitatively for the presence of protein, glucose, bilirubin, nitrite, blood and ketones and the pH was measured. Quantitative analyses were undertaken for osmolality, urea, creatinine and glucose. The results of the analyses were generally unremarkable with the exceptions of pH, glucose and in some cases the urea/creatinine ratios. However, with the exception of the glucose these other results are physiologically normal. One possible explanation for the presence of glucose in the urine of the okapis is dietary. In the wild these animals are folivorous and thus they may not be able to cope with the high level of sugar presented to them in their captive diet. However, it must be emphasised that this condition has no apparent ill effects on the animals which are in good health and are breeding successfully.

Porphyrin synthesis in blood cells of patients with erythropoietic protoporphyria

The protoporphyrin accumulation observed in the red blood cells of patients with erythropoietic protoporphyria can be explained by decreased activity of the enzyme heme synthetase or by increased production of porphyrins in the affected cells. In literature experimental evidence both for a partial heme synthetase deficiency and for increased porphyrin biosynthesis has been presented. In a group of ten patients with erythropoietic protoporphyria the biosynthesis of porphyrins from delta-aminolevulinic acid and from glycine-succinic acid appeared to be normal in peripheral blood cells. These results are consistent with the partial heme synthetase deficiency previously found to be the basic defect of this disease.