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

Severe acute respiratory syndrome coronavirus 2, primary varicella zoster virus coinfection, and a polymicrobial ventilator-associated tracheobronchitis in an adult immunocompetent male: a case report

BACKGROUND: The spectrum of clinical manifestations and differential diagnosis associated with coronavirus disease 2019 is broad, ranging from fever and cutaneous eruptions to respiratory distress or even neurological disorders. Coexisting multipathogen infections significantly increase the complexity of the proper diagnostic and therapeutic approach and correlate with the rate of intensive care unit admissions and in-hospital mortality. CASE PRESENTATION: We present a case of multipathogen respiratory infection with severe acute respiratory syndrome coronavirus 2, varicella zoster virus, and polymicrobial tracheobronchitis in a 48-year-old Caucasian male hospitalized after traumatic brain injury. The patient tested positive for severe acute respiratory syndrome coronavirus 2 infection upon admission. During his stay in the intensive care unit, the patient developed a vesicular exanthema along with respiratory failure and signs of septic shock. CONCLUSION: This case of an adult presenting with severe acute respiratory syndrome coronavirus 2 infection and simultaneous primary varicella zoster virus infection illustrates the importance of considering coinfections in patients with coronavirus disease 2019 with unusual clinical manifestations

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

Variability of Neural Activation During Walking in Humans: Short Heels and Big Calves

People come in different shapes and sizes. In particular, calf muscle size in humans varies considerably. One possible cause for the different shapes of calf muscles is the inherent difference in neural signals sent to these muscles during walking. In sedentary adults, the variability in neural control of the calf muscles was examined with muscle size, walking kinematics and limb morphometrics. Half the subjects walked while activating their medial gastrocnemius (MG) muscles more strongly than their lateral gastrocnemius (LG) muscles during most walking speeds (‘MG-biased’). The other subjects walked while activating their MG and LG muscles nearly equally (‘unbiased’). Those who walked with an MG-biased recruitment pattern also had thicker MG muscles and shorter heel lengths, or MG muscle moment arms, than unbiased walkers, but were similar in height, weight, lower limb length, foot length, and exhibited similar walking kinematics. The relatively less plastic skeletal system may drive calf muscle size and motor recruitment patterns of walking in humans