Detection of aberrant gene expression events in RNA sequencing data.

RNA sequencing (RNA-seq) has emerged as a powerful approach to discover disease-causing gene regulatory defects in individuals affected by genetically undiagnosed rare disorders. Pioneering studies have shown that RNA-seq could increase the diagnosis rates over DNA sequencing alone by 8-36%, depending on the disease entity and tissue probed. To accelerate adoption of RNA-seq by human genetics centers, detailed analysis protocols are now needed. We present a step-by-step protocol that details how to robustly detect aberrant expression levels, aberrant splicing and mono-allelic expression in RNA-seq data using dedicated statistical methods. We describe how to generate and assess quality control plots and interpret the analysis results. The protocol is based on the detection of RNA outliers pipeline (DROP), a modular computational workflow that integrates all the analysis steps, can leverage parallel computing infrastructures and generates browsable web page reports.

Childhood obesity study: a pilot study of the effect of the nutrition education program Color My Pyramid.

The need for successful nutrition interventions is critical as the prevalence of childhood obesity increases. Thus, this pilot project examines the effect of a nutrition education program, Color My Pyramid, on children's nutrition knowledge, self-care practices, activity levels, and nutrition status. Using a pretest-posttest, quasiexperimental design, 126 fourth- and fifth-grade students from experimental and control schools are compared. The intervention program incorporates an online component www.MyPyramid.gov, Orem's Self-Care Deficit Nursing Theory, and consists of six classes taught over a 3-month period. Results indicated that the program increased nutrition knowledge in the control group. Furthermore, it increased activity time from pretest to posttest and decreased systolic blood pressure for children in both groups; however, there were no significant differences in BMI percentiles. The findings indicate that Color My Pyramid can be successfully employed in school settings and thus support school nursing practice.

School reentry for children with cancer: perceptions of nurses, school personnel, and parents.

The purpose of this interdisciplinary descriptive study was to examine the perceptions of nurses, school personnel, and parents about school reentry for children with cancer and to determine whether activities and services performed supported school reentry. The study also investigated parents' perception of the impact of cancer on their child's academic performance, cognitive ability, and school attendance. Results of the study showed that few activities and services were performed to facilitate children's school reentry by either nurses or school personnel. Parents reported no significant differences in their children's cognitive ability or academic performance. School attendance was significantly lower after diagnosis and therapy. Conclusions were that communication among nurses, school personnel, and parents was a major barrier to providing effective services to students and their parents. Nurses were unsure of how to help parents navigate the school bureaucracy, school personnel felt they needed more information, and parents felt that their children were not receiving all the school reentry services needed. Individuals in this study recommended that a liaison position be created to coordinate services.

Tobacco use triggers for mothers of infants: implications for pediatric nursing practice.

PURPOSE: To extend current knowledge of tobacco use by exploring whether subsets of mothers of infants have unique triggers for smoking relapse during the early stages of becoming a mother. METHOD: Using data from a study of smoking relapse among mothers of infants (N = 133), comparative analyses were conducted for groups formed on the basis of their intention to be nonsmokers after delivery (yes/no) and their actual smoking behavior during the first 2 weeks of infant life (yes/no). FINDINGS: The identified groups of mothers were found to be significantly different from one another in several ways, including self-reports that their baby's crying episodes caused them to think about smoking and their level of self-confidence to not smoke as response to infant crying. CONCLUSIONS: Pediatric nurses in primary and acute care settings are in a unique position to support mothers for whom the challenge of handling infant cry episodes is a trigger for smoking behavior. Interventions that teach mothers how to cope with infant irritability are likely to support the smoking cessation efforts, and consequently, interrupt the intergenerational cycle of tobacco-related maternal and child health morbidities.