Context dependent substitution biases vary within the human genome

Background: Models of sequence evolution typically assume that different nucleotide positions evolve independently. This assumption is widely appreciated to be an over-simplification. The best known violations involve biases due to adjacent nucleotides. There have also been suggestions that biases exist at larger scales, however this possibility has not been systematically explored. Results: To address this we have developed a method which identifies over- and under-represented substitution patterns and assesses their overall impact on the evolution of genome composition. Our method is designed to account for biases at smaller pattern sizes, removing their effects. We used this method to investigate context bias in the human lineage after the divergence from chimpanzee. We examined bias effects in substitution patterns between 2 and 5 bp long and found significant effects at all sizes. This included some individual three and four base pair patterns with relatively large biases. We also found that bias effects vary across the genome, differing between transposons and non-transposons, between different classes of transposons, and also near and far from genes. Conclusions: We found that nucleotides beyond the immediately adjacent one are responsible for substantial context effects, and that these biases vary across the genome

Does nonmedical hospital admission staff accurately triage emergency department patients?

OBJECTIVES: Utilization of hospital emergency departments (EDs) is continuously increasing. Though nurses and physicians are ultimately responsible for the definite triage decisions, initial ED patient triage is frequently performed by hospital admission staff. This study analyzes the quality of assessment of the severity of emergencies and the choice of treatment unit made by hospital admission staff. METHODS: One thousand fifty-nine consecutive surgical and medical patients entering the ED of the University Hospital Basel during an 11-day period were independently assessed by hospital admission staff without formal medical training, ED nursing staff, and ED physicians. Emergencies were classified by severity (intervention within minutes/hours/days) or by severity and resource utilization (immediate intervention with/without life-threatening condition, delayed intervention with high/low/no demand of resources). Emergency assessment and triage decision (surgical/medical, outpatient/inpatient treatment) were documented independently by all three ED staff groups. RESULTS: In 64% of the cases, initial assessment by admission staff corresponded with the final assessment by the ED physician. Concordance was, however, poor (kappa=0.23). Underestimation of the severity occurred in 7.5% of cases without severe or lethal consequences. Ninety-four percent of patients were treated in the unit to which they were originally triaged by the admission staff. CONCLUSION: Triage quality regarding the choice of treatment unit was found to be excellent, whereas the quality of the assessment of the severity of the emergency by nonmedical ED admission staff was acceptable. ED patients have to be assessed by medical staff early after admission to ensure adequate and timely interventions