Codon context is an important feature of gene primary structure that modulates mRNA decoding accuracy. We have developed an analytical software package and a graphical interface for comparative codon context analysis of all the open reading frames in a genome (the ORFeome). Using the complete ORFeome sequences of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans and Escherichia coli, we show that this methodology permits large-scale codon context comparisons and provides new insight on the rules that govern the evolution of codon-pair context.

OBJECTIVE: To investigate current prevalence of pain among different musician groups, sex, and body region. METHODS: Studies were sought from PubMed, Web of Science, Academic Search Complete, Science Direct, and Scielo. Databases were searched from 1 January 2000 until December 2012. Two reviewers screened titles and abstracts and assessed full reports for potentially eligible studies. One reviewer extracted information on musicians’ characteristics, study methods, and study quality. When possible, a meta-analysis of pain prevalence estimates was performed. RESULTS: A total of 18 studies were included in this systematic review. Studies assessed pain prevalence in general and the prevalence of pain affecting playing capacity for different time periods: point, 1-week, 1-year, month, and lifetime prevalence. The prevalence of pain in general, across all groups of musicians and periods of interest over which pain was assessed, varied between 29.0 and 90.0%, whereas the prevalence of pain affecting playing capacity varied between 25.8 and 84.4%. There was a tendency for guitar players to have the highest pain prevalence. The most affected body regions were the low back (9.8 to 66.7%) and neck (9.8 to 48.5%). CONCLUSIONS: Pain prevalence is high among musicians, independent of the pain definition and time period used. Health and educational policy makers should become aware of the high prevalence of pain affecting performance practices, so that pain-associated mechanisms are investigated and preventive strategies are tested and implemented.

Motivation: DNA sequences can be represented by sequences of four symbols, but it is often useful to convert the symbols into real or complex numbers for further analysis. Several mapping schemes have been used in the past, but they seem unrelated to any intrinsic characteristic of DNA. The objective of this work was to find a mapping scheme directly related to DNA characteristics and that would be useful in discriminating between different species. Mathematical models to explore DNA correlation structures may contribute to a better knowledge of the DNA and to find a concise DNA description. Results: We developed a methodology to process DNA sequences based on inter-nucleotide distances. Our main contribution is a method to obtain genomic signatures for complete genomes, based on the inter-nucleotide distances, that are able to discriminate between different species. Using these signatures and hierarchical clustering, it is possible to build phylogenetic trees. Phylogenetic trees lead to genome differentiation and allow the inference of phylogenetic relations. The phylogenetic trees generated in this work display related species close to each other, suggesting that the inter-nucleotide distances are able to capture essential information about the genomes. To create the genomic signature, we construct a vector which describes the inter-nucleotide distance distribution of a complete genome and compare it with the reference distance distribution, which is the distribution of a sequence where the nucleotides are placed randomly and independently. It is the residual or relative error between the data and the reference distribution that is used to compare the DNA sequences of different organisms. Contact:vera@ua.pt

The continuous development of resuscitation techniques and intensive care reduced the mortality rate induced by the initial shock in burn patients and, currently, infections (especially sepsis) are the main causes of mortality of these patients. The misuse of antimicrobial agents is strongly related to antimicrobial and adverse patient outcomes, development of microbial resistance and increased healthcare-related costs. To overcome these risks, antimicrobial stewardship is mandatory and biomarkers are useful to avoid unnecessary medical prescription, to monitor antimicrobial therapy and to support the decision of its stop. Among a large array of laboratory tests, procalcitonin (PCT) emerged as the leading biomarker to accurately and time-effectively indicate the presence of systemic infection. In the presence of systemic infection, PCT blood levels undergo a sudden and dramatic increase, following the course of the infection, and quickly subside after the control of the septic process. This work is a meta-analysis on PCT performance as a biomarker for sepsis. This meta–analysis showed that overall pooled area under the curve (AUC) is 0.83 (95% CI = 0.76 to 0.90); the estimated cut-off is 1.47 ng/mL. The overall sepsis effect in PCT levels is significant and strong (Cohen's d is 2.1 and 95% CI = 1.1 to 3.2). This meta–analysis showed PCT may be considered as a biomarker with a strong diagnostic ability to discriminate between the septic from the non-septic burn patients. Thus, this work encourages the determination of PCT levels in clinical practice for the management of these patients, in order to timely identify the susceptibility to sepsis and to initiate the antimicrobial therapy, improving the patients’ outcomes.