Genome-wide binding analysis of 195 DNA binding proteins reveals "reservoir" promoters and human specific SVA-repeat family regulation.

A key aspect in defining cell state is the complex choreography of DNA binding events in a given cell type, which in turn establishes a cell-specific gene-expression program. Here we wanted to take a deep analysis of DNA binding events and transcriptional output of a single cell state (K562 cells). To this end we re-analyzed 195 DNA binding proteins contained in ENCODE data. We used standardized analysis pipelines, containerization, and literate programming with R Markdown for reproducibility and rigor. Our approach validated many findings from previous independent studies, underscoring the importance of ENCODE's goals in providing these reproducible data resources. We also had several new findings including: (i) 1,362 promoters, which we refer to as 'reservoirs,' that are defined by having up to 111 different DNA binding-proteins localized on one promoter, yet do not have any expression of steady-state RNA (ii) Reservoirs do not overlap super-enhancer annotations and distinct have distinct properties from super-enhancers. (iii) The human specific SVA repeat element may have been co-opted for enhancer regulation and is highly transcribed in PRO-seq and RNA-seq. Collectively, this study performed by the students of a CU Boulder computational biology class (BCHM 5631 -Spring 2020) demonstrates the value of reproducible findings and how resources like ENCODE that prioritize data standards can foster new findings with existing data in a didactic environment.

Three-dimensional printing and virtual surgery for congenital heart procedural planning.

Complex unrepaired congenital heart disease requires extensive planning to determine the optimal procedural approach. Conventional noninvasive diagnostic imaging initially provides only two-dimensional (2D) representations of the complex, three-dimensional cardiovascular anatomy. With the expansion of 3D visualization techniques in imaging, a paradigm shift has occurred in complex congenital heart disease surgical planning using digital and 3D printed heart models. There has been early success in demonstrating the benefit of these models in interdisciplinary communication and education. The future goal of this work is to demonstrate a clinical outcome benefit using digital and 3D printed models to plan both surgical and catheterization-based interventional procedures. Ultimately, the hope is that advanced procedural planning with virtual surgery and 3D printing will enhance decision-making in complex congenital heart disease cases resulting in improved perioperative performance by reducing operative times, complications, and reoperations.

Osteopathic manipulative treatment for inpatients with pulmonary exacerbations of cystic fibrosis: effects on spirometry findings and patient assessments of breathing, anxiety, and pain.

CONTEXT: Osteopathic manipulative treatment (OMT) has been studied in patients with various respiratory diseases. However, to the authors' knowledge, no studies have assessed the efficacy of OMT in patients with cystic fibrosis (CF). OBJECTIVE: To evaluate pulmonary function and perceptions of breathing, anxiety, and pain of CF patients who receive OMT in addition to standard inpatient management of pulmonary exacerbation. METHODS: In a single-blind randomized controlled trial, we assessed adult patients with a history of CF who were admitted to the hospital because of pulmonary exacerbation. Participants were randomly assigned to receive a daily standardized protocol of OMT or sham therapy. Both groups also received standard treatment for CF. Spirometry and questionnaire data (self-assessment of breathing, pain, and anxiety level) were collected before the first OMT or sham therapy session and after the final session. RESULTS: A total of 33 patients were included in the study: 16 in the OMT group and 17 in the sham therapy group. Improvements in spirometric parameters were observed in both the OMT and the sham therapy groups, with no statistically significant differences found between the groups. More patients in the OMT group than in the sham therapy group had questionnaire response patterns that indicated their breathing had improved during the study period (15 of 16 vs 8 of 16, respectively). No differences were found between groups for perceived improvement of pain and anxiety. CONCLUSION: In the current study, CF patients who received OMT did not demonstrate statistically significant differences in pre- and posttreatment spirometry findings compared with CF patients who received sham therapy. Questionnaire findings suggest that OMT may affect CF patients' perception of overall quality of breathing. Additional studies are needed to assess the clinical use of OMT in patients with CF.