Reliability of measurements performed by community-drawn anthropometrists from rural Ethiopia

Background

Undernutrition is an important risk factor for childhood mortality, and remains a major problem facing many developing countries. Millennium Development Goal 1 calls for a reduction in underweight children, implemented through a variety of interventions. To adequately judge the impact of these interventions, it is important to know the reproducibility of the main indicators for undernutrition. In this study, we trained individuals from rural communities in Ethiopia in anthropometry techniques and measured intra- and inter-observer reliability.

Methods and Findings

We trained 6 individuals without prior anthropometry experience to perform weight, height, and middle upper arm circumference (MUAC) measurements. Two anthropometry teams were dispatched to 18 communities in rural Ethiopia and measurements performed on all consenting pre-school children. Anthropometry teams performed a second independent measurement on a convenience sample of children in order to assess intra-anthropometrist reliability. Both teams measured the same children in 2 villages to assess inter-anthropometrist reliability. We calculated several metrics of measurement reproducibility, including the technical error of measurement (TEM) and relative TEM. In total, anthropometry teams performed measurements on 606 pre-school children, 84 of which had repeat measurements performed by the same team, and 89 of which had measurements performed by both teams. Intra-anthropometrist TEM (and relative TEM) were 0.35 cm (0.35%) for height, 0.05 kg (0.39%) for weight, and 0.18 cm (1.27%) for MUAC. Corresponding values for inter-anthropometrist reliability were 0.67 cm (0.75%) for height, 0.09 kg (0.79%) for weight, and 0.22 kg (1.53%) for MUAC. Inter-anthropometrist measurement error was greater for smaller children than for larger children.

Conclusion

Measurements of height and weight were more reproducible than measurements of MUAC and measurements of larger children were more reliable than those for smaller children. Community-drawn anthropometrists can provide reliable measurements that could be used to assess the impact of interventions for childhood undernutrition.     

Performance of local light microscopy and the ParaScreen Pan/Pf rapid diagnostic test to detect malaria in health centers in Northwest Ethiopia

Background

Diagnostic tests are recommended for suspected malaria cases before treatment, but comparative performance of microscopy and rapid diagnostic tests (RDTs) at rural health centers has rarely been studied compared to independent expert microscopy.

Methods

Participants (N = 1997) with presumptive malaria were recruited from ten health centers with a range of transmission intensities in Amhara Regional State, Northwest Ethiopia during October to December 2007. Microscopy and ParaScreen Pan/Pf® RDT were done immediately by health center technicians. Blood slides were re-examined later at a central laboratory by independent expert microscopists.

Results

Of 1,997 febrile patients, 475 (23.8%) were positive by expert microscopists, with 57.7% P.falciparum, 24.6% P.vivax and 17.7% mixed infections. Sensitivity of health center microscopists for any malaria species was >90% in five health centers (four of which had the highest prevalence), >70% in nine centers and 44% in one site with lowest prevalence. Specificity for health center microscopy was very good (>95%) in all centers. For ParaScreen RDT, sensitivity was ≥90% in three centers, ≥70% in six and <60% in four centers. Specificity was ≥90% in all centers except one where it was 85%.

Conclusions

Health center microscopists performed well in nine of the ten health centers; while for ParaScreen RDT they performed well in only six centers. Overall the accuracy of local microscopy exceeded that of RDT for all outcomes. This study supports the introduction of RDTs only if accompanied by appropriate training, frequent supervision and quality control at all levels. Deficiencies in RDT use at some health centers must be rectified before universal replacement of good routine microscopy with RDTs. Maintenance and strengthening of good quality microscopy remains a priority at health center level.     

Obesity Modulates the Association among APOE Genotype,Insulin, and Glucose in Men

Objective: Obesity, insulin resistance, and apolipoprotein E (APOE) genotype have all been associated with coronary heart disease. We examined the interaction between obesity and APOE genotype in determining fasting insulin and glucose levels. Research Methods and Procedures: From 1991 to 1995, 3799 subjects underwent a clinical examination and fasting insulin and glucose measurement. APOE genotypes were determined on 3500 participants. Participants taking oral hypoglycemic drugs or insulin preparations or with the rare APOE2/4 genotype were excluded. Finally, 2929 individuals were included in the present analysis. Results: In men, we observed a statistically significant interaction between obesity and APOE genotype on insulin and glucose level (p = 0.003 and 0.008, respectively). Obese men with the APOE4 genotype presented with higher levels of insulin and glucose than obese men in the other genotype groups. No association between genotype and insulin or glucose in nonobese men was observed. Obesity was associated with higher insulin levels in the three APOE genotypes groups, whereas obesity was directly associated with glucose in those with the APOE4 genotype. In women, the effect of interaction between APOE genotype and obesity on fasting insulin and glucose was not statistically significant. Obesity was associated with higher levels of fasting insulin and glucose. APOE genotype was not associated with insulin or glucose. Discussion: Obesity modulates the association between the APOE genotype and fasting insulin and glucose levels in men. Although weight control is important in all people, it may be especially important in APOE4 men to modify potentially elevated fasting insulin and glucose levels.     

The diversity and distribution of lianas in the Afromontane rain forests of Ethiopia

The diversity and distribution of lianas were studied in five Afromontane rain forests of Ethiopia. Quadrats of 20 × 20 m were laid down along transects in the Bonga, Berhane‐Kontir, Harenna, Yayu and Maji forests. In all forests, 30,917 liana individuals belonging to 123 species in 87 genera and 40 plant families were recorded. The most species‐rich families were Asclepiadaceae (14), Fabaceae (9), Annonaceae (7) and Cucurbitaceae (7). The top 10 dominant families represented 56% of the total number of species. Over 400 other plant species representing different life forms were recorded growing together with lianas. The lianas accounted for over 30% of the total woody plant diversity and over 20% of the total floral diversity in the study areas. The analysis of floristic composition of the forests indicates that the Berhane‐Kontir Forest had the highest Fisher's diversity index α, and Yayu the lowest. Generally, there were low similarities between the forests in terms of species composition. Although lianas were abundant in almost all forests, there was a considerable variation among the forests in terms of density and spatial distribution. The major dispersal modes of lianas were anemochory (30%), mammaliochory (30%), ornithochory and autochory, and the four mechanisms of climbing of lianas were twining (54%), hooking (24%), rooting and use of tendrils. Altitude and human disturbance were found to be important factors affecting liana distribution. The need for sustainable management and use of lianas in the Afromontane rain forests is emphasized.     

Singular value decomposition-based regression identifies activation of endogenous signaling pathways in vivo

Background

The physical organization and chromosomal localization of genes within genomes is known to play an important role in their function. Most genes arise by duplication and move along the genome by random shuffling of DNA segments. Higher order structuring of the genome occurs in eukaryotes, where groups of physically linked genes are co-expressed. However, the contribution of gene duplication to gene order has not been analyzed in detail, as it is believed that co-expression due to recent duplicates would obscure other domains of co-expression.

Results

We have catalogued ordered duplicated genes in Drosophila melanogaster, and found that one in five of all genes is organized as tandem arrays. Furthermore, among arrays that have been spatially conserved over longer periods than would be expected on the basis of random shuffling, a disproportionate number contain genes encoding developmental regulators. Using in situ gene expression data for more than half of the Drosophila genome, we find that genes in these conserved clusters are co-expressed to a much higher extent than other duplicated genes.

Conclusions

These results reveal the existence of functional constraints in insects that retain copies of genes encoding developmental and regulatory proteins as neighbors, allowing their co-expression. This co-expression may be the result of shared cis-regulatory elements or a shared need for a specific chromatin structure. Our results highlight the association between genome architecture and the gene regulatory networks involved in the construction of the body plan.     

Abundance,Species Composition and Spatial Distribution of Planktonic Rotifers and Crustaceans in Lake Ziway (Rift Valley,Ethiopia)

Species composition, abundance, and spatial distribution of rotifer and crustacean zooplankton were studied in Lake Ziway from late April to early July 2004. A total of 49 rotifer species was recorded, with Anuraeopsis fissa, Brachionus angularis, Filinia novaezealandiae, and Trichocerca ruttneri being numerically dominant. Variation in abundance was extremely high, ranging from 2 to 1000+ individuals per litre. There was no significant difference in the distribution of rotifer species between inshore and offshore regions. Crustacean species richness was low, with only five cladoceran and three copepod species occurring in the open water. Moina micrura and Diaphanosoma excisum dominated the cladoceran community, whereas Thermocyclops decipiens was the dominant copepod. Although numerically dominant (75%), rotifers accounted for less than 30% of mean total zooplankton biomass. Peak abundance of crustaceans was observed in May and June, following the onset of the rainy season and increased phytoplankton production. Variation in the spatial distribution of crustacean species was neither observed horizontally between inshore and offshore areas nor vertically in the highly turbid and wind exposed deeper part of the lake. On the other hand, Moina micrura varied significantly in size between inshore and offshore areas. Adult M. micrura dominated offshore, whereas juveniles were more abundant inshore, suggesting a predominantly littoral selective predation on large and adult crustaceans by fish. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Rational design of novel, potent piperazinone and imidazolidinone BACE1 inhibitors

Guided by structure-based design, we synthesized two novel series of potent inhibitors of BACE1 and generated extensive SAR around both the prime and non-prime side binding pockets. The key feature of both series is a cyclic amine motif specifically crafted to achieve interactions with both the flap and with the S2' pocket.     

Modeling genetic inheritance of copy number variations

Copy number variations (CNVs) are being used as genetic markers or functional candidates in gene-mapping studies. However, unlike single nucleotide polymorphism or microsatellite genotyping techniques, most CNV detection methods are limited to detecting total copy numbers, rather than copy number in each of the two homologous chromosomes. To address this issue, we developed a statistical framework for intensity-based CNV detection platforms using family data. Our algorithm identifies CNVs for a family simultaneously, thus avoiding the generation of calls with Mendelian inconsistency while maintaining the ability to detect de novo CNVs. Applications to simulated data and real data indicate that our method significantly improves both call rates and accuracy of boundary inference, compared to existing approaches. We further illustrate the use of Mendelian inheritance to infer SNP allele compositions in each of the two homologous chromosomes in CNV regions using real data. Finally, we applied our method to a set of families genotyped using both the Illumina HumanHap550 and Affymetrix genome-wide 5.0 arrays to demonstrate its performance on both inherited and de novo CNVs. In conclusion, our method produces accurate CNV calls, gives probabilistic estimates of CNV transmission and builds a solid foundation for the development of linkage and association tests utilizing CNVs.     

Prospects for sustainable use and development of wild food plants in Ethiopia

Field and herbarium studies on wild flowering plants of Ethiopia furnished 203 species consumed by the community. These account for about 3% of the higher plant species in the country and comprise herbs (37%), shrubs (32%), and trees (31%). Species with edible fruits contributed to 61.6%, leaves 27.7%, stems 14.4%, roots 13.3%, and seeds 10.3%. About 15% are considered famine foods. Forest habitats gave 102 species, woodlands 99, grasslands 83, bushlands 52, rocky and dry areas 47, cultivated places 41, riverbanks 31, and roadsides/ disturbed areas 25. The altitudinal distribution gave 148 species between 1500-2400 m, 144 below 1500 m and 81 above 2400 m a.s.l. Some species are wild and others slightly or strongly associated with humans, revealing a living analogue of the wild-semiwild-domesticated continuum. Full-scale ethnobotanical studies, implementing appropriate conservation measures and domesticating and integrating promising taxa into existing crops are favored for the purpose of diversification of food sources, ensuring food security, and maintenance of biodiversity and environmental integrity.     

N-acetylglucosamine and glucosamine-containing arabinogalactan proteins control somatic embryogenesis

In plants, complete embryos can develop not only from the zygote, but also from somatic cells in tissue culture. How somatic cells undergo the change in fate to become embryogenic is largely unknown. Proteins, secreted into the culture medium such as endochitinases and arabinogalactan proteins (AGPs) are required for somatic embryogenesis. Here we show that carrot (Daucus carota) AGPs can contain glucosamine and N-acetyl-D-glucosaminyl and are sensitive to endochitinase cleavage. To determine the relevance of this observation for embryogenesis, an assay was developed based on the enzymatic removal of the cell wall from cultured cells. The resulting protoplasts had a reduced capacity for somatic embryogenesis, which could be partially restored by adding endochitinases to the protoplasts. AGPs from culture medium or from immature seeds could fully restore or even increase embryogenesis. AGPs pretreated with chitinases were more active than untreated molecules and required an intact carbohydrate constituent for activity. AGPs were only capable of promoting embryogenesis from protoplasts in a short period preceding cell wall reformation. Apart from the increase in embryogenesis, AGPs can reinitiate cell division in a subpopulation of otherwise non-dividing protoplasts. These results show that chitinase-modified AGPs are extracellular matrix molecules able to control or maintain plant cell fate.