A scalable and memory-efficient algorithm for de novo transcriptome assembly of non-model organisms

Abstract Background With increased availability of de novo assembly algorithms, it is feasible to study entire transcriptomes of non-model organisms. While algorithms are available that are specifically designed for performing transcriptome assembly from high-throughput sequencing data, they are very memory-intensive, limiting their applications to small data sets with few libraries. Results We develop a transcriptome assembly algorithm that recovers alternatively spliced isoforms and expression levels while utilizing as many RNA-Seq libraries as possible that contain hundreds of gigabases of data. New techniques are developed so that computations can be performed on a computing cluster with moderate amount of physical memory. Conclusions Our strategy minimizes memory consumption while simultaneously obtaining comparable or improved accuracy over existing algorithms. It provides support for incremental updates of assemblies when new libraries become available

A scalable and memory-efficient algorithm for de novo transcriptome assembly of non-model organisms

Abstract Background With increased availability of de novo assembly algorithms, it is feasible to study entire transcriptomes of non-model organisms. While algorithms are available that are specifically designed for performing transcriptome assembly from high-throughput sequencing data, they are very memory-intensive, limiting their applications to small data sets with few libraries. Results We develop a transcriptome assembly algorithm that recovers alternatively spliced isoforms and expression levels while utilizing as many RNA-Seq libraries as possible that contain hundreds of gigabases of data. New techniques are developed so that computations can be performed on a computing cluster with moderate amount of physical memory. Conclusions Our strategy minimizes memory consumption while simultaneously obtaining comparable or improved accuracy over existing algorithms. It provides support for incremental updates of assemblies when new libraries become available

Blood Pressure and Cardiovascular Responses to Emergency Calls in Volunteer Firefighters and Emergency Medical Technicians

Hypertension and obesity are both primary risk factors for cardiovascular (CV) disease. Among the firefighter (FF) population cardiac events remain the leading cause of line-of-duty deaths. Work related stress can cause a surge in heart rate and blood pressure (BP) and studies have noted that FF and Emergency Medical Technicians (EMTs) have increased heart rate and BP throughout the day. Thus, understanding the risk factors associated with work related stress in FF and EMTs, including BP surges and CV disease risk are important factors in continual need of study

Effects of circuit exercise training on vascular health and blood pressure

As the global burden of cardiovascular disease (CVD) rises, public health-related interventions aimed at prevention of heart disease have gained medical attention. Clinical research reports that exercise is a protective risk factor associated with CVD and that clinicians need to provide exercise recommendations to patients. Nevertheless, physical inactivity remains a public health problem. In certain populations, like firefighters (FF), increased risk of CVD is especially concerning. The workload FF face is extreme, 50% of line-of-duty deaths (LODD) in FF are cardiac-related, and research on the volunteer FF population is scarce. Government regulations do not require volunteer FF companies to have fitness testing or programming, so exercise intervention studies are necessary to improve the burden of CVD risk in this population. Therefore, this study examined the effects of a 4-week exercise circuit training (CT) intervention on vascular health and fitness in volunteer FF (N = 27) from the Philadelphia PA area compared to a control group of Non-FF (N = 25). Carotid artery intima-media thickness (IMT), brachial artery flow-mediated dilation (FMD), augmentation index, and pulse pressure (PP), brachial and central blood pressure (BP) and fitness were measured pre- and post- intervention. Overall, volunteer FF had more significant improvements (p < 0.05) in vascular health measures (FMD, IMT, and PP). In both groups, we also found that brachial and central BP decreased with exercise. We show that a 4 week CT program can improve vascular structure and function in the volunteer FF population, suggesting that clinicians may be able to reduce or prevent cardiac LODD by exercise. Keywords: Vascular health, Flow-mediated dilation, Blood pressure, Exercise, Carotid artery intima media thickness, Volunteer firefighter

Comparison of 4 Weeks of Circuit Training Versus Resistance Training in Middle-Aged Adults

Despite significant progress, cardiovascular (CV) disease remains the leading killer in the US, with lack of physical activity being a primary risk factor. Research suggests that 4 weeks of exercise training reduces blood pressure (BP) and fat mass, as well as improves fitness; yet it is unclear whether circuit training (CT) or resistance training (RT) yields better short-term improvements