aRNApipe: a balanced, efficient and distributed pipeline for processing RNA-seq data in high-performance computing environments.

SUMMARY: The wide range of RNA-seq applications and their high-computational needs require the development of pipelines orchestrating the entire workflow and optimizing usage of available computational resources. We present aRNApipe, a project-oriented pipeline for processing of RNA-seq data in high-performance cluster environments. aRNApipe is highly modular and can be easily migrated to any high-performance computing (HPC) environment. The current applications included in aRNApipe combine the essential RNA-seq primary analyses, including quality control metrics, transcript alignment, count generation, transcript fusion identification, alternative splicing and sequence variant calling. aRNApipe is project-oriented and dynamic so users can easily update analyses to include or exclude samples or enable additional processing modules. Workflow parameters are easily set using a single configuration file that provides centralized tracking of all analytical processes. Finally, aRNApipe incorporates interactive web reports for sample tracking and a tool for managing the genome assemblies available to perform an analysis. AVAILABILITY AND DOCUMENTATION: https://github.com/HudsonAlpha/aRNAPipe ; DOI: 10.5281/zenodo.202950. CONTACT: rmyers@hudsonalpha.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Measurement of arterial occlusion pressure using straight and curved blood flow restriction cuffs.

Arterial occlusion pressure (AOP) is influenced by the characteristics of the cuff used to measure AOP. Doppler ultrasound was used to measure AOP of the brachial and superficial femoral arteries using straight and curved blood flow restriction cuffs in 21 males and 21 females. Vessel diameter and blood flow were evaluated as independent predictors of AOP. Overall, there were no significant differences in AOP when using the straight and curved cuffs in the brachial (129 mmHg vs. 128 mmHg) or superficial femoral artery (202 mmHg vs. 200 mmHg), respectively. Overall, AOP was greater (p < 0.05) in males than in females in the arm (135 mmHg, 123 mmHg) and leg (211 mmHg, 191 mmHg). Brachial (0.376 mm, 0.323 mm) and superficial femoral (0.547 mm, 0.486 mm) arteries were larger (p = 0.016) in males than in females, respectively. Systolic blood pressure (SBP) and arm circumference were predictive of brachial artery AOP, whereas SBP, diastolic blood pressure, thigh circumference, and vessel diameter were predictive of superficial femoral artery AOP. Straight and curved cuffs are efficacious in the measurement of AOP in the arm and leg. Differences in vessel size may contribute to sex differences in AOP but this requires further investigation.