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Background There is a significant difference between synonymous codon usage in many organisms, and it is known that codons used more frequently generally showed efficient decoding rate. At the gene level, however, there are conflicting reports on the existence of a correlation between codon adaptation and translation efficiency, even in the same organism. Results To resolve this issue, we cultured Escherichia coli under conditions designed to maintain constant levels of mRNA and protein and subjected the cells to ribosome profiling (RP) and mRNA-seq analyses. We showed that the RP results correlated more closely with protein levels generated under similar culture conditions than with the mRNA abundance from the mRNA-seq. Our result indicated that RP/mRNA ratio could be used as a measure of translation efficiency at gene level. On the other hand, the RP data showed that codon-specific ribosome density at the decoding site negatively correlated with codon usage, consistent with the hypothesis that preferred codons display lower ribosome densities due to their faster decoding rate. However, highly codon-adapted genes showed higher ribosome densities at the gene level, indicating that the efficiency of translation initiation, rather than higher elongation efficiency of preferred codons, exerted a greater effect on ribosome density and thus translation efficiency. Conclusions These findings indicate that evolutionary pressure on highly expressed genes influenced both codon bias and translation initiation efficiency and therefore explains contradictory findings that codon usage bias correlates with translation efficiency of native genes, but not with the artificially created gene pool, which was not subjected to evolution pressure. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1115) contains supplementary material, which is available to authorized users.

OBJECTIVE There have been no previous studies about consultation of the bereaved who have lost a loved one to cancer and ask for medical help. The aim of this study was to investigate their basic characteristics and their psychiatric disorders. METHODS A retrospective study using clinical and background data obtained over 30 months (from April 2007 to September 2009) was conducted at outpatient services for bereaved families at the Department of Psycho-Oncology at Saitama Medical University International Medical Center, Japan. RESULTS During the period of investigation, 51 patients underwent consultation. The patients were frequently female (P < 0.0001) and the spouse of the deceased. Regarding the psychiatric diagnoses, major depression was the most common (39%), followed by adjustment disorders (28%). CONCLUSIONS This study revealed basic characteristics and psychiatric disorders of the bereaved who asked for medical help. Most of the patients were women (86.3%) and 86.3% of them received a psychiatric diagnosis. This information is important for both physicians and psychologists since the bereaved who have lost a loved one to cancer often ask for medical help in clinical settings.