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1.  Relationships between paediatricians and infant formula milk companies 
Archives of Disease in Childhood  2006;91(5):383-385.
Paediatricians should recognise the influence of infant formula milk companies and avoid intentionally or inadvertently promoting them
doi:10.1136/adc.2005.072892
PMCID: PMC2082719  PMID: 16632663
breast feeding; conflict of interest; infant formula; nutrition
2.  Contact burns from hair straighteners: a new hazard in the home 
This series highlights a previously unreported hazard for children within the home, hair straightening irons. Thermal injury is a common reason for presentation at the emergency department. Contact burns from domestic irons and hair curling tongs are well documented in the literature. We have become aware of this new hazard in the home, which has resulted in several presentations to our department with deep partial thickness or full thickness burns.
doi:10.1136/emj.2005.027094
PMCID: PMC2464438  PMID: 16498145
burns; hair straighteners; children
4.  Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species 
Genome Biology  2006;7(8):R75.
A codon usage table for 32 nematode species is presented and suggests that total genomic GC content drives codon usage.
Background
Codon usage has direct utility in molecular characterization of species and is also a marker for molecular evolution. To understand codon usage within the diverse phylum Nematoda, we analyzed a total of 265,494 expressed sequence tags (ESTs) from 30 nematode species. The full genomes of Caenorhabditis elegans and C. briggsae were also examined. A total of 25,871,325 codons were analyzed and a comprehensive codon usage table for all species was generated. This is the first codon usage table available for 24 of these organisms.
Results
Codon usage similarity in Nematoda usually persists over the breadth of a genus but then rapidly diminishes even within each clade. Globodera, Meloidogyne, Pristionchus, and Strongyloides have the most highly derived patterns of codon usage. The major factor affecting differences in codon usage between species is the coding sequence GC content, which varies in nematodes from 32% to 51%. Coding GC content (measured as GC3) also explains much of the observed variation in the effective number of codons (R = 0.70), which is a measure of codon bias, and it even accounts for differences in amino acid frequency. Codon usage is also affected by neighboring nucleotides (N1 context). Coding GC content correlates strongly with estimated noncoding genomic GC content (R = 0.92). On examining abundant clusters in five species, candidate optimal codons were identified that may be preferred in highly expressed transcripts.
Conclusion
Evolutionary models indicate that total genomic GC content, probably the product of directional mutation pressure, drives codon usage rather than the converse, a conclusion that is supported by examination of nematode genomes.
doi:10.1186/gb-2006-7-8-r75
PMCID: PMC1779591
5.  AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis 
BMC Bioinformatics  2006;7:275.
Background
The invariant lineage of the nematode Caenorhabditis elegans has potential as a powerful tool for the description of mutant phenotypes and gene expression patterns. We previously described procedures for the imaging and automatic extraction of the cell lineage from C. elegans embryos. That method uses time-lapse confocal imaging of a strain expressing histone-GFP fusions and a software package, StarryNite, processes the thousands of images and produces output files that describe the location and lineage relationship of each nucleus at each time point.
Results
We have developed a companion software package, AceTree, which links the images and the annotations using tree representations of the lineage. This facilitates curation and editing of the lineage. AceTree also contains powerful visualization and interpretive tools, such as space filling models and tree-based expression patterning, that can be used to extract biological significance from the data.
Conclusion
By pairing a fast lineaging program written in C with a user interface program written in Java we have produced a powerful software suite for exploring embryonic development.
doi:10.1186/1471-2105-7-275
PMCID: PMC1501046  PMID: 16740163

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